WO2022241480A1 - Méthodes et compositions pour le traitement d'infections virales - Google Patents

Méthodes et compositions pour le traitement d'infections virales Download PDF

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Publication number
WO2022241480A1
WO2022241480A1 PCT/US2022/072329 US2022072329W WO2022241480A1 WO 2022241480 A1 WO2022241480 A1 WO 2022241480A1 US 2022072329 W US2022072329 W US 2022072329W WO 2022241480 A1 WO2022241480 A1 WO 2022241480A1
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Prior art keywords
protein
virus
viral
receptor
fragment
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PCT/US2022/072329
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English (en)
Inventor
Roee Amit
Sarah GOLDBERG
Naor GRANIK
Nanami KIKUCHI
Or WILLINGER
Patricia Kitchen
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Technion Research & Development Foundation Limited
Benevira Inc.
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Application filed by Technion Research & Development Foundation Limited, Benevira Inc. filed Critical Technion Research & Development Foundation Limited
Priority to AU2022273065A priority Critical patent/AU2022273065A1/en
Priority to CA3218711A priority patent/CA3218711A1/fr
Priority to IL308478A priority patent/IL308478A/en
Priority to EP22808557.7A priority patent/EP4337174A1/fr
Publication of WO2022241480A1 publication Critical patent/WO2022241480A1/fr
Priority to US18/507,493 priority patent/US20240218024A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C07K14/08—RNA viruses
    • C07K14/165—Coronaviridae, e.g. avian infectious bronchitis virus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/76—Viruses; Subviral particles; Bacteriophages
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/08—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite containing oxygen, e.g. ethers, acetals, ketones, quinones, aldehydes, peroxides
    • A61K47/10—Alcohols; Phenols; Salts thereof, e.g. glycerol; Polyethylene glycols [PEG]; Poloxamers; PEG/POE alkyl ethers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/30—Macromolecular organic or inorganic compounds, e.g. inorganic polyphosphates
    • A61K47/42—Proteins; Polypeptides; Degradation products thereof; Derivatives thereof, e.g. albumin, gelatin or zein
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/14—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles
    • A61K9/16—Agglomerates; Granulates; Microbeadlets ; Microspheres; Pellets; Solid products obtained by spray drying, spray freeze drying, spray congealing,(multiple) emulsion solvent evaporation or extraction
    • A61K9/1605—Excipients; Inactive ingredients
    • A61K9/1629—Organic macromolecular compounds
    • A61K9/1658—Proteins, e.g. albumin, gelatin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/85—Fusion polypeptide containing an RNA binding domain
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2795/00—Bacteriophages
    • C12N2795/00011—Details
    • C12N2795/18011—Details ssRNA Bacteriophages positive-sense
    • C12N2795/18111—Leviviridae
    • C12N2795/18122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention is in the field of therapeutic and prophylactic treatments, as well as protein expression.
  • SARS-CoV-2 virions enters the host cells via interaction between the receptor binding domain of the viral Spike protein (RBD), and hACE2 on the host cell surface. Characterization and inhibition of RBD-hACE2 binding are cmcial to three different aspects of controlling the pandemic. First, it is necessary to rapidly quantify the hACE2 binding affinity of naturally-arising RBD mutants in order to assess the impact of these mutants on viral transmission and case load.
  • RBD viral Spike protein
  • the RBD has been shown to harbor multiple epitopes and is thus a main component in many of the current SARS-CoV-2 vaccines currently being developed and used whether in inactivated (Sinovac), DNA (Astrazeneca), mRNA (Pfizer/BioNtech and Moderna), or protein (Novavax) form.
  • inhibition of RBD-hACE2 interaction could protect healthy host cells at early stages of infection and is therefore a desired property of candidate therapeutics.
  • an assay that quantifies RBD-hACE2 interaction, and enables rapid identification of small molecules that inhibit RBD-hACE2 interaction, is of great interest.
  • a cell-free assay for screening of inhibitors of protein-protein interaction should satisfy the following requirements: detection using standard lab equipment, repeatability, ease of use, flexibility, and low cost. Since protein sizes are well below the optical diffraction limit, some form of bulk measurement is required.
  • RBD-hACE2 inhibitors Commercial Chemical, Cat. 502050
  • a cell-free option available for screening RBD-hACE2 inhibitors consists of an antibody-coated surface that binds antigen-RBD.
  • Horseradish peroxidase (HRP)-hACE2 is introduced in the presence or absence of an inhibitor candidate. Excess HRP-hACE2 is rinsed, and HRP signal is developed and measured at 450 nm via plate reader.
  • HRP horseradish peroxidase
  • RNA- protein granules that form a structured complex having RNA, e.g., noncoding RNA with hairpins, on the exterior of the granule, and therapeutic agents, such as a human receptor that can bind to a virus of interest, fused to a bacteriophage coat protein.
  • the phage coat protein binds to the RNA via non-coding hairpins, thus forming an ordered complex.
  • the granules dissipate in an ordered way whereby the therapeutic agent is released for treatment or as a prophylactic for a therapy, e.g., to treat or prevent a viral infection.
  • a soluble ACE2 fragment that can be used in an RNA-protein granule disclosed herein or as a single agent (i.e., non-complexed) for treatment or as a prophylactic.
  • Such therapeutic agents disclosed herein may be delivered using a microneedle array, e.g., in a patch for intradermal delivery.
  • the present invention provides soluble fusion proteins comprising an extracellular domain of a human receptor or a fragment thereof and a bacteriophage coat protein, as well as synthetic microcarriers comprising a solid support conjugated to a plurality of viral proteins or fragments thereof.
  • Nucleic acid molecules and vectors encoding the soluble fusion protein, synthetic RNA-protein granules comprising a fusion protein, as well as method using the soluble fusion protein and/or the synthetic microcarriers are also provided.
  • a soluble fusion protein comprising an extracellular domain of a human receptor or a fragment thereof and a first bacteriophage coat protein.
  • the fragment is a functional fragment capable of protein or ligand binding.
  • the fusion protein is devoid of a transmembrane domain.
  • the extracellular domain of the human receptor devoid of the first bacteriophage coat protein when exogenously expressed in human cells in culture is present in a low titer in media from the human cells.
  • poorly expressed is an expression of less than 1 mg per ml of human cell culture media at confluence.
  • the human receptor binds a viral protein.
  • the human receptor is Angiotensin converting enzyme 2 (ACE2).
  • ACE2 Angiotensin converting enzyme 2
  • the ACE2 comprises the amino acid sequence provided in SEQ ID NO: 3.
  • the coat protein is a capsid protein.
  • the bacteriophage is the PP7 bacteriophage.
  • the PP7 coat protein comprises the amino acid sequence provided in SEQ ID NO: 4.
  • the soluble fusion protein further comprises a second bacteriophage coat protein.
  • the soluble fusion protein comprises a tandem dimer of the bacteriophage coat protein.
  • the first and second bacteriophage coat proteins are the same protein.
  • the first and second bacteriophage coat proteins are separated by a linker.
  • the extracellular domain of a human receptor or a fragment thereof is N-terminal to the first bacteriophage coat protein.
  • the soluble fusion protein further comprises a fluorescent protein domain.
  • the fluorescent protein domain is between the extracellular domain of a human receptor or a fragment thereof and the bacteriophage coat protein.
  • the extracellular domain of a human receptor or a fragment thereof and the fluorescent protein domain are separated by a linker
  • the fluorescent protein domain and the bacteriophage coat protein are separated by a linker
  • the extracellular domain of a human receptor or a fragment thereof and the bacteriophage coat protein are separated by a linker or a combination thereof.
  • the soluble fusion protein further comprises an affinity tag.
  • the affinity tag is a His tag, is a C-terminal tag or both.
  • the fusion protein comprises, from N-terminus to C-terminus, the extracellular domain of a human receptor or a fragment thereof, a fluorescent protein domain, a tandem dimer of the bacteriophage coat protein and an affinity tag.
  • the human receptor is ACE2; b. the fluorescent protein is mCherry; c. the tandem dimer comprises two copies of a PP7 coat protein; d. the affinity tag is a His tag; or e. a combination thereof.
  • the soluble fusion protein comprises or consists of the amino acid sequence provided in SEQ ID NO: 10.
  • nucleic acid molecule comprising a coding region encoding a soluble fusion protein of the invention.
  • the nucleic acid molecule of the invention comprises a first sequence encoding the first bacteriophage coat protein and a second sequence encoding the second bacteriophage coat protein wherein the first and second bacteriophage coat proteins comprise the same amino acid sequence and wherein the first and second sequences comprise different nucleotide sequences.
  • an expression vector comprising a nucleic acid molecule of the invention.
  • the expression vector is configured to express the soluble fusion protein from human cells.
  • a method of expressing a soluble form of an extracellular domain of a human receptor or a fragment thereof from a cell comprising: a. providing an expression vector comprising a coding region, suitable to induce expression of a protein encoded by the coding region in the cell, wherein the coding region encodes a fusion protein comprising the extracellular domain of a human receptor or a fragment thereof and a bacteriophage coat protein; and b. introducing the expression vector into the cell; thereby expressing an extracellular domain of a human receptor or a fragment thereof from a cell.
  • the fusion protein is a fusion protein of the invention, or the expression vector is an expression vector of the invention.
  • the cell is a human cell.
  • the method is a method of expressing a difficult to express human receptor or a fragment thereof.
  • a difficult to express human receptor or a fragment thereof is a human receptor or a fragment thereof that when expressed not as the fusion protein is expressed at less than 50% of the expression when expressed as the fusion protein.
  • RNA-protein granule comprising: a. a fusion protein comprising an extracellular domain of a human receptor or a fragment thereof and a first bacteriophage coat protein; and b. a synthetic RNA molecule comprising a plurality of binding sites of the first bacteriophage coat protein.
  • the fusion protein is a soluble fusion protein of the invention.
  • a synthetic microcarrier comprising a synthetic solid support conjugated to a plurality of viral proteins or fragments thereof capable of protein binding.
  • the solid support is a bead.
  • the bead is a polystyrene bead.
  • the solid support is a fluorescent solid support.
  • the solid support comprises a diameter of between 0.25 and 1 ⁇ M.
  • the solid support comprises a diameter of between 0.7 and 1 ⁇ M.
  • the viral protein expressed on the surface of virions is expressed on the surface of virions.
  • the viral protein is a viral peplomer.
  • the fragment comprises a receptor binding domain (RBD).
  • RBD receptor binding domain
  • the viral protein is a SARS-CoV-2 protein.
  • the synthetic microcarrier comprises at least 10,000 viral proteins or fragments thereof conjugated thereto.
  • the solid support comprises free functional groups and the viral proteins or fragments thereof are conjugated to the free function groups.
  • the functional groups are carboxyl groups.
  • the viral proteins or fragments thereof are conjugated to the solid support by a carbodiimide crosslinking reaction.
  • the synthetic microcarrier is for use in testing an inhibitor of virus binding.
  • a method of selecting an effective antiviral therapeutic designed to inhibit binding of a viral protein to its target non-viral protein comprising: a. providing a synthetic microcarrier of the invention comprising the viral protein or a fragment thereof capable of binding the target non-viral protein; b. contacting the synthetic microcarrier with the target non-viral protein or a fragment thereof capable of binding the viral protein in the presence of the antiviral therapeutic and in the absence of the antiviral therapeutic, and c.
  • the synthetic microcarrier comprises a viral peplomer or receptor binding fragment thereof and the non-viral protein is a receptor used by the virus to enter cells.
  • the non-viral protein or fragment thereof comprises or is conjugated to a detectable moiety and the measuring binding comprises detection of the detectable moiety from the synthetic microcarrier.
  • the detecting comprises isolating the synthetic microcarrier and detecting the non-viral protein or fragment thereof on the synthetic microcarrier.
  • the detecting comprises microscopy analysis of the microcarriers and detecting colocalization of the non-viral protein or fragment thereof and the synthetic microcarrier.
  • the synthetic microcarrier comprises or is conjugated to a first fluorescent moiety and the non-viral protein or fragment thereof comprises or is conjugated to a second fluorescent moiety and the detecting comprises detecting overlapping fluorescence from the first and second moieties.
  • the detectable moiety is a fluorophore and wherein the detection comprises flow cytometric analysis of the synthetic microcarriers for fluorescence from the fluorophore.
  • the contacting is in the presence of a blocking agent that inhibits non-specific binding to the synthetic microcarrier.
  • the non-viral protein is a soluble fusion protein of the invention.
  • the microcarrier comprises a SARS-CoV-2 spike protein or a fragment comprising a spike protein RBD and the non-viral protein is ACE2.
  • the contacting is in the presence of 5 -10 ⁇ g BSA per 1 pi. of synthetic microcarrier, is for between 30-60 minutes or both.
  • the decrease is a. a statistically significant decrease; b. a decrease to below a predetermined threshold of binding; c. a decrease of at least 10%; or d. a combination thereof.
  • a method of testing binding of an agent to a viral protein or a fragment thereof comprising: a. providing a synthetic microcarrier of the invention comprising the viral protein or a fragment thereof; b. contacting the synthetic microcarrier with the agent; and c. detecting binding of the synthetic microcarrier to the agent; thereby testing binding of an agent to a viral protein or a fragment thereof.
  • the detecting comprises isolating the synthetic microcarrier and detecting the agent or isolating the agent and detecting the synthetic microcarrier.
  • the detecting comprises microscopy analysis of the microcarriers and detecting the agent at the microcarrier.
  • the microcarrier comprises or is conjugated to a first fluorescent moiety
  • the agent comprises or is conjugated to a second fluorescent moiety
  • the detecting comprises detecting colocalized fluorescence from the first and second moieties.
  • the agent comprises a fluorophore and the detecting comprises flow cytometric analysis of the microcarrier for fluorescence from the fluorophore.
  • the agent is selected from: a. an antibody or antigen binding fragment against the viral protein or a fragment thereof; b. a small molecule designed to bind to the viral protein or a fragment thereof; c. a synthetic peptide designed to bind to the viral protein or a fragment thereof; and d. a synthetic RNA-protein granule comprising any one of (a-c) or a natural peptide that binds the viral protein or a fragment thereof.
  • a method of testing binding of an extracellular domain or fragment thereof of a human receptor to a target comprising: a. providing a soluble fusion protein of the invention comprising the extracellular domain or fragment thereof of the human receptor; b. contacting the soluble fusion protein with the target; and c. detecting binding of the soluble fusion protein to the target; thereby testing binding of an extracellular domain or fragment thereof of a human receptor to a target.
  • the detecting comprises isolating the target and detecting the soluble fusion protein or isolating the soluble fusion protein and detecting the target.
  • the target is immobilized on a solid support and the soluble fusion protein comprises a fluorophore and the detecting comprises detecting fluorescence from the fluorophore at the solid support.
  • the solid support is a bead and the detecting comprises flow cytometric analysis of the bead for fluorescence from the fluorophore.
  • the target is a ligand of the human receptor.
  • a synthetic RNA-protein granule comprising (a) a fusion protein comprising a therapeutic protein, and a first bacteriophage coat protein, wherein the first bacteriophage coat protein is an RNA binding protein (RBP); and (b) a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RNA-protein granule comprising (a) a fusion protein comprising a viral protein, a variant, and/or a fragment thereof, and a first bacteriophage coat protein, wherein the first bacteriophage coat protein is an RNA binding protein (RBP); and (b) a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RBP RNA binding protein
  • the granule comprises a fusion protein comprising one or more variants of the viral protein, and the first bacteriophage coat protein.
  • the viral protein is a spike protein.
  • the viral protein is an envelope protein.
  • the granule further comprises fusion proteins comprising viral proteins from one or more additional viruses.
  • the viral protein is a protein from a virus selected from the group consisting of an Arenaviridae virus, a Bomaviridae virus, a Bunyaviridae virus, a Caliciviridae virus, Coronaviridae virus, a Deltavirus virus, a Filoviridae virus, a Flaviviridae virus, Lentiviridae virus, an Orthomyxoviridae virus, a Paramyxoviridae virus, a Picomaviridae virus, a Pneumoviridae virus, a Polyomaviridae virus, a Retro viridae virus, a Rhabdoviridae virus, or a Togaviridae virus.
  • the viral protein is the spike protein of SARS-CoV-2 or a variant thereof.
  • RNA-protein granule comprising: (a) a fusion protein comprising an extracellular domain of a human receptor or a fragment thereof, and a first bacteriophage coat protein, wherein the first bacteriophage is an RNA binding protein (RBP); and (b) a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RBP RNA binding protein
  • said extracellular domain of the human receptor is devoid of a transmembrane domain.
  • said fragment is a functional fragment.
  • said human receptor binds a viral protein.
  • the human receptor is selected from the group consisting of ACE2, APN, AXL, BST/tetherin, CCR5, CD4, CD14, CD21, CD35, CDHR3, Coxsackie and Adenovirus Receptor (CAR), CXCR4, DC-SIGN, DC-SIGNR, DPP4, EGFR, a glycosaminoglycan, GRP78, heat shock protein 70, heat shock protein 90, hMGL, human mannose receptor, ICAM-1, an integrin, KREMEN1, LamR, LDLR, lectin, MAG, MDA5, Mer, NMMHC-IIA, NTCP, nucleolin, PDGFRa, PDGFRa, PILRa, RIG-I, a sialic acid receptor, TIM-1, TIM-4, TLR3, and Tyro3.
  • the viral protein is a protein from a virus selected from the group consisting of an Arenaviridae virus, a Bomaviridae virus, a Bunyaviridae virus, a Caliciviridae virus, Coronaviridae virus, a Deltavirus virus, a Filoviridae virus, a Flaviviridae virus, Fentiviridae virus, an Orthomyxoviridae virus, a Paramyxoviridae virus, a Picomaviridae virus, a Pneumoviridae virus, a Polyomaviridae virus, a Retro viridae virus, a Rhabdoviridae virus, or a Togaviridae virus.
  • a virus selected from the group consisting of an Arenaviridae virus, a Bomaviridae virus, a Bunyaviridae virus, a Caliciviridae virus, Coronaviridae virus, a Deltavirus virus, a Filoviridae virus, a
  • the viral protein is a protein from a virus selected from the group consisting of a human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacoranovirus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Vims A6, A10, or A16), dengue virus, Ebola virus, Epstein- Barr virus (EBV), hepatitis A virus (hepatoviru)s, hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John Cunning
  • said first bacteriophage coat protein is a PP7 bacteriophage coat protein.
  • said PP7 bacteriophage coat protein comprises the amino acid sequence provided in SEQ ID NO: 4.
  • said first bacteriophage coat protein is an MS2 bacteriophage coat protein, a Q ⁇ -bacteriophage coat protein, or a GA bacteriophage coat protein.
  • the synthetic RNA molecule comprises at least three hairpins; at least four hairpins; at least five hairpins; at least 8 hairpins; or at least 10 hairpins.
  • the synthetic RNA molecule is a synthetic long non-coding RNA (slncRNA).
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by the bacteriophage coat protein, wherein the at least three hairpins are separated by a randomized sequences that does not encode a particular protein or structure. In some embodiments, the randomized sequences do not encode a hairpin.
  • the granule is semi-permeable.
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by the first bacteriophage coat protein, wherein the at least three hairpins are each separated by a randomized sequence encoding a hairpin that does not have an encoding an RNA binding motif recognized by the first bacteriophage coat protein.
  • the granule is non-permeable.
  • the synthetic RNA-protein granule has a cross-linked RNA shell such that the therapeutic or the fusion protein is on the interior of the synthetic RNA- protein granule.
  • the synthetic RNA-protein granule dissolves upon administration to a human subject in less than about 5 hours, in less than about 10 hours, in less than a day, in 1-25 days, or in 1-10 days.
  • RNA-protein granule provided herein to the subject.
  • the subject is a human subject.
  • the human subject has or is at risk of having a viral infection.
  • the synthetic RNA-protein granule is administered to the human subject to prevent a viral infection.
  • the viral infection is caused by a virus selected from a human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BKpolyomavirus, Alphacoronavirus, Betacorano virus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Virus A6, A10, or A16), dengue virus, Ebola virus, Epstein-Barr virus (EBV), hepatitis A virus (hepatovirus), hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John Cunningham virus (JC virus), rhinovirus,
  • a virus selected from
  • RNA-protein granule provided herein to the subject.
  • the coronavirus disease is caused by infection with SARS-CoV-2.
  • the synthetic RNA-protein granule is administered to the human subject orally, intranasally, subcutaneously, or transdermally.
  • a pharmaceutical formulation comprising bovine serum albumin (BSA), PEG, PLGA, an IgG, or any combination thereof, and a synthetic RNA-protein granule provided herein.
  • a pharmaceutical formulation comprising the synthetic RNA-protein granule provided herein, wherein the formulation is a hydrogel.
  • the hydrogel is an aqueous glycerin-hydrogel.
  • a liquid pharmaceutical formulation comprising an effective amount of the synthetic RNA-protein granule provided herein, and a pharmaceutically acceptable carrier, wherein the formulation is suitable for intranasal administration or for administration as a throat spray.
  • microneedle array comprising a pharmaceutical formulation provided herein.
  • a microneedle array comprising a synthetic RNA- protein granule provided herein.
  • a patch for intradermal delivery to a human subject said patch comprising a microneedle array provided herein.
  • an isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37.
  • a method of treating a human subject infected with SARS-CoV-2 or a human subject at risk of being infected with SARS-CoV-2 comprising administering a protein provided herein to the human subject (e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37).
  • a protein provided herein to the human subject (e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37).
  • a method of preventing coronavirus disease in a human subject in need thereof comprising administering a protein provided herein (e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37) to the human subject.
  • a protein provided herein e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37
  • the protein is administered to the human subject intradermally.
  • a pharmaceutical composition comprising a protein provided herein (e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37), and a pharmaceutically acceptable carrier.
  • a protein provided herein e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37
  • a pharmaceutically acceptable carrier e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37
  • a microneedle array comprising a protein provided herein (e.g., isolated protein encoding soluble human ACE2, wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37).
  • a patch comprising a microneedle array provided herein.
  • a method of treating a human subject infected with SARS-CoV-2 or a human subject at risk of being infected with SARS-CoV-2 comprising applying a microneedle array provided herein or a patch provided herein to the human subject.
  • a method of preventing coronavirus disease in a human subject in need thereof comprising applying a microneedle array provided herein or a patch provided herein to the human subject.
  • a soluble fusion protein comprising an extracellular domain of a human receptor or a fragment thereof and a first bacteriophage coat protein, wherein the first bacteriophage coat protein is an RNA binding protein (RBP).
  • RBP RNA binding protein
  • said fragment is a functional fragment capable of protein or ligand binding.
  • said fusion protein is devoid of a transmembrane domain of the human receptor.
  • said extracellular domain of said human receptor is devoid of said first bacteriophage coat protein when exogenously expressed in human cells in culture is present in a low titer in media from said human cells.
  • said human receptor binds a viral protein.
  • the human receptor is selected from the group consisting of ACE2, APN, AXL, BST/tetherin, CCR5, CD4, CD14, CD21, CD35, CDHR3, Coxsackie and Adenovirus Receptor (CAR), CXCR4, DC-SIGN, DC-SIGNR, DPP4, EGFR, a glycosaminoglycan, GRP78, heat shock protein 70, heat shock protein 90, hMGL, human mannose receptor, ICAM-1, an integrin, KREMEN1, LamR, LDLR, lectin, MAG, MDA5, Mer, NMMHC-IIA, NTCP, nucleolin, PDGFRa, PDGFRa, PILRa, RIG-I, a sialic acid receptor, TIM-1, TIM-4, TLR3, and Tyro3.
  • CAR Adenovirus Receptor
  • the viral protein is expressed on the surface of a virus, wherein the virus is selected from a human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacoranovirus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Vims A6, A10, or A16), dengue virus, Ebola virus, Epstein- Barr virus (EBV), hepatitis A virus (hepatoviru)s, hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John
  • said human receptor is Angiotensin converting enzyme 2 (ACE2).
  • ACE2 comprises the amino acid sequence provided in SEQ ID NO: 3.
  • said coat protein is a bacteriophage coat protein is an MS2, a Q ⁇ , or a lambda bacteriophage coat protein.
  • said bacteriophage is a PP7 bacteriophage (e.g., comprising a PP7 coat protein).
  • said PP7 coat protein comprises the amino acid sequence provided in SEQ ID NO: 4.
  • the soluble fusion protein further comprises a second bacteriophage coat protein. In some embodiments, the soluble fusion protein further comprises a tandem dimer of said bacteriophage coat protein. In some embodiments, said first and second bacteriophage coat proteins are the same protein. In some embodiments, said first and second bacteriophage coat proteins are separated by a linker.
  • said extracellular domain of a human receptor or a fragment thereof is N-terminal to said first bacteriophage coat protein.
  • the soluble fusion protein further comprises a fluorescent protein domain.
  • said fluorescent protein domain is between said extracellular domain of a human receptor or a fragment thereof and said bacteriophage coat protein.
  • said extracellular domain of a human receptor or a fragment thereof and said fluorescent protein domain are separated by a linker
  • said fluorescent protein domain and said bacteriophage coat protein are separated by a linker
  • said extracellular domain of a human receptor or a fragment thereof and said bacteriophage coat protein are separated by a linker or a combination thereof.
  • the soluble fusion protein further comprises an affinity tag.
  • said affinity tag is a His tag, is a C-terminal tag or both.
  • said fusion protein comprises, from N-terminus to C- terminus, said extracellular domain of a human receptor or a fragment thereof, a fluorescent protein domain, a tandem dimer of said bacteriophage coat protein and an affinity tag.
  • said human receptor is ACE2; said fluorescent protein is mCherry; said tandem dimer comprises two copies of a PP7 coat protein; said affinity tag is a His tag; or a combination thereof.
  • the soluble fusion protein comprises or consists of the amino acid sequence provided in SEQ ID NO: 10.
  • nucleic acid molecule comprising a coding region encoding a soluble fusion protein provided herein.
  • the nucleic acid molecule comprises a first sequence encoding said first bacteriophage coat protein and a second sequence encoding said second bacteriophage coat protein wherein said first and second bacteriophage coat proteins comprise the same amino acid sequence and wherein said first and second sequences comprise different nucleotide sequences.
  • an expression vector comprising a nucleic acid molecule provided herein.
  • the expression vector is configured to express said soluble fusion protein from human cells.
  • a method of expressing a soluble form of an extracellular domain of a human receptor or a fragment thereof from a cell comprising: providing an expression vector comprising a coding region, suitable to induce expression of a protein encoded by said coding region in said cell, wherein said coding region encodes a fusion protein comprising said extracellular domain of a human receptor or a fragment thereof and a bacteriophage coat protein; and introducing said expression vector into said cell; thereby expressing an extracellular domain of a human receptor or a fragment thereof from a cell.
  • said fusion protein is a fusion protein provided herein or said expression vector is an expression vector provided herein.
  • said cell is a human cell.
  • said method is a method of expressing a difficult to express human receptor or a fragment thereof.
  • a difficult to express human receptor or a fragment thereof is a human receptor or a fragment thereof that when expressed not as said fusion protein is expressed at less than 50% of the expression when expressed as said fusion protein.
  • a synthetic microcarrier comprising a synthetic solid support conjugated to a plurality of viral proteins or fragments thereof capable of protein binding.
  • said solid support is a bead.
  • said bead is a polystyrene bead.
  • said solid support is a fluorescent solid support.
  • said solid support comprises a diameter of between 0.25 and 1 ⁇ M. In some embodiments, said solid support comprises a diameter of between 0.7 and 1 pM.
  • said viral protein expressed on the surface of virions is expressed on the surface of virions.
  • said viral protein is a viral peplomer.
  • said fragment comprises a receptor binding domain (RBD).
  • RBD receptor binding domain
  • said viral protein is a SARS-CoV-2 protein.
  • the synthetic microcarrier comprises at least 10,000 viral proteins or fragments thereof conjugated thereto.
  • said solid support comprises free functional groups and said viral proteins or fragments thereof are conjugated to said free function groups.
  • said functional groups are carboxyl groups.
  • said viral proteins or fragments thereof are conjugated to said solid support by a carbodiimide crosslinking reaction.
  • the synthetic microcarrier is for use in testing an inhibitor of virus binding.
  • a method of selecting an effective antiviral therapeutic designed to inhibit binding of a viral protein to its target non-viral protein comprising: providing a synthetic microcarrier provided herein comprising said viral protein or a fragment thereof capable of binding said target non-viral protein; contacting said synthetic microcarrier with said target non-viral protein or a fragment thereof capable of binding said viral protein in the presence of said antiviral therapeutic and in the absence of said antiviral therapeutic, and measuring binding of said non-viral protein or a fragment thereof to said microcarrier both in the presence and absence of said antiviral therapeutic, wherein a decrease in binding of said non-viral protein or fragment thereof to said synthetic microcarrier in the presence of said antiviral therapeutic as compared to the absence of said antiviral therapeutic indicates said antiviral therapeutic is effective; thereby selecting an effective antiviral therapeutic.
  • said synthetic microcarrier comprises a viral peplomer or receptor binding fragment thereof and said non-viral protein is a receptor used by said virus to enter cells.
  • said non-viral protein or fragment thereof comprises or is conjugated to a detectable moiety and said measuring binding comprises detection of said detectable moiety from said synthetic microcarrier.
  • said detecting comprises isolating said synthetic microcarrier and detecting said non-viral protein or fragment thereof on said synthetic microcarrier.
  • said detecting comprises microscopy analysis of said microcarriers and detecting colocalization of said non-viral protein or fragment thereof and said synthetic microcarrier.
  • said synthetic microcarrier comprises or is conjugated to a first fluorescent moiety and said non-viral protein or fragment thereof comprises or is conjugated to a second fluorescent moiety and said detecting comprises detecting overlapping fluorescence from said first and second moieties.
  • said detectable moiety is a fluorophore and wherein said detection comprises flow cytometric analysis of said synthetic microcarriers for fluorescence from said fluorophore.
  • said contacting is in the presence of a blocking agent that inhibits non-specific binding to said synthetic microcarrier.
  • said non-viral protein is a soluble fusion protein provided herein.
  • said microcarrier comprises a SARS-CoV-2 spike protein or a fragment comprising a spike protein RBD and said non-viral protein is ACE2.
  • said contacting is in the presence of 5 -10 ⁇ g BSA per 1 pi of synthetic microcarrier, is for between 30-60 minutes or both.
  • said decrease is a statistically significant decrease; a decrease to below a predetermined threshold of binding; a decrease of at least 10%; or a combination thereof.
  • a method of testing binding of an agent to a viral protein or a fragment thereof comprising: providing a synthetic microcarrier provided herein comprising said viral protein or a fragment thereof; contacting said synthetic microcarrier with said agent; and detecting binding of said synthetic microcarrier to said agent; thereby testing binding of an agent to a viral protein or a fragment thereof.
  • said detecting comprises isolating said synthetic microcarrier and detecting said agent or isolating said agent and detecting said synthetic microcarrier.
  • said detecting comprises microscopy analysis of said microcarriers and detecting said agent at said microcarrier.
  • said microcarrier comprises or is conjugated to a first fluorescent moiety
  • said agent comprises or is conjugated to a second fluorescent moiety
  • said detecting comprises detecting colocalized fluorescence from said first and second moieties.
  • said agent comprises a fluorophore and said detecting comprises flow cytometric analysis of said microcarrier for fluorescence from said fluorophore.
  • said agent is selected from: an antibody or antigen binding fragment against said viral protein or a fragment thereof; a small molecule designed to bind to said viral protein or a fragment thereof; a synthetic peptide designed to bind to said viral protein or a fragment thereof; and a synthetic RNA-protein granule comprising any one of (a-c) or a natural peptide that binds said viral protein or a fragment thereof.
  • a method of testing binding of an extracellular domain or fragment thereof of a human receptor to a target comprising: providing a soluble fusion protein provided herein comprising said extracellular domain or fragment thereof of said human receptor; contacting said soluble fusion protein with said target; and detecting binding of said soluble fusion protein to said target; thereby testing binding of an extracellular domain or fragment thereof of a human receptor to a target.
  • said detecting comprises isolating said target and detecting said soluble fusion protein or isolating said soluble fusion protein and detecting said target.
  • said target is immobilized on a solid support and said soluble fusion protein comprises a fluorophore and said detecting comprises detecting fluorescence from said fluorophore at said solid support.
  • said solid support is a bead and said detecting comprises flow cytometric analysis of said bead for fluorescence from said fluorophore.
  • said target is a ligand of said human receptor.
  • RNA binding protein RBP
  • RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein
  • the human receptor is selected from the group consisting of ACE2, APN, AXL, BST/tetherin, CCR5, CD4, CD14, CD21, CD35, CDHR3, Coxsackie and Adenovirus Receptor (CAR), CXCR4, DC-SIGN, DC-SIGNR, DPP4, EGFR, a glycosaminoglycan, GRP78, heat shock protein 70, heat shock protein 90, hMGL, human mannose receptor, ICAM-1, an integrin, KREMEN1, LamR, LDLR, lectin, MAG, MDA5, Mer, NMMHC-IIA, NTCP, nucleolin, PDGFRa, PDGFRa, PILRa, RIG-I, a sialic acid receptor, TIM-1, TIM-4, TLR3, and Tyro3.
  • CAR Adenovirus Receptor
  • the viral protein is a protein from a virus selected from the group consisting of an Arenaviridae virus, a Bomaviridae virus, a Bunyaviridae virus, a Caliciviridae virus, Coronaviridae virus, a Deltavirus virus, a Filoviridae virus, a Flaviviridae virus, Lentiviridae virus, an Orthomyxoviridae virus, a Paramyxoviridae virus, a Picomaviridae virus, a Pneumoviridae virus, a Polyomaviridae virus, a Retro viridae virus, a Rhabdoviridae virus, or a Togaviridae virus.
  • said human receptor is Angiotensin converting enzyme 2 (ACE2).
  • ACE2 comprises the amino acid sequence provided in SEQ ID NO: 3.
  • a method of preventing a viral infection in a human subject at risk thereof comprising applying a microneedle array to the human subject.
  • the microneedle array comprises a therapeutically effective amount of a synthetic RNA-protein granule
  • the synthetic RNA-protein granule comprises: a fusion protein comprising a viral protein that is expressed on the surface of a virus, or a functional fragment thereof, and a first bacteriophage coat protein, wherein the a first bacteriophage is an RNA binding protein (RBP); and a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RBP RNA binding protein
  • the viral protein is a protein from a virus selected from the group consisting of a human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacorano virus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Virus A6, A10, or A16), dengue virus, Ebola virus, Epstein- Barr virus (EBV), hepatitis A virus (hepatovirus), hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John Cunningham virus (JC
  • the viral protein is a SARS-CoV-2 spike protein.
  • the synthetic RNA-protein granule comprises a plurality of fusion proteins each comprising the viral protein that is expressed on the surface of a virus, or a variant of said viral protein.
  • said first bacteriophage coat protein is a PP7 bacteriophage coat protein.
  • said PP7 bacteriophage coat protein comprises the amino acid sequence provided in SEQ ID NO: 4.
  • said first bacteriophage coat protein is an MS2 bacteriophage coat protein, a Q ⁇ -bacteriophage coat protein, a GA bacteriophage coat protein, or a lambda phage coat protein.
  • the synthetic RNA-protein granule further comprises a second bacteriophage coat protein.
  • the second bacteriophage coat protein is a coat protein selected from the group consisting or PP7, GA, MS2, Q ⁇ , or a lambda phage coat protein.
  • the synthetic RNA molecule comprises at least three hairpins; at least four hairpins; at least five hairpins; at least 8 hairpins; at least 10 hairpins, at least 12 hairpins; at least 14 hairpins; at least 16 hairpins; at least 18 hairpins; at least 20 hairpins; or at least 25 hairpins.
  • the synthetic RNA molecule is a synthetic long non-coding RNA (slncRNA).
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by the first bacteriophage coat protein, wherein the at least three hairpins are separated by a randomized sequence that does not encode a particular protein or structure.
  • the randomized sequences do not encode a hairpin.
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by the bacteriophage coat protein, wherein the at least three hairpins are each separated by a randomized sequence encoding a hairpin that does not have an encoding an RNA binding motif recognized by the first bacteriophage coat protein.
  • the microneedle array is in a patch for intradermal delivery of the synthetic RNA-protein granule to the human subject.
  • Figures 1A and IB Schematic of the v-particle binding assay. (Fig. 1A) RBD
  • receptor binding domain is covalently attached to fluorescent polystyrene particles, yielding virion-like particles (v-particles).
  • V-particles are incubated with hACE2F in the presence and absence of a candidate inhibitor.
  • Inhibitor activity is measured by the decrease in the red fluorescence (fluorescent unit or “F.U.”) of the v-particles, due to reduced hACE2F binding.
  • FIG. 2A Fine graph showing fluorescence of v-particles bound non- specifically by mCherry, as a function of BSA concentration. BSA is added to the reactions to prevent non-specific binding. The optimal amount of BSA was determined to be 5-10 ⁇ g per 1 pi. v-particle stock (reactions in this assay contained 2 pi. v-particle stock).
  • FIG. 2B Scatter plot showing fluorescence of v-particles as a function of reaction time. 45 min is sufficient for binding reactions.
  • FIG. 2C Scatter plot showing sensitivity of v-particle - hACE2F binding. As low as -0.1 ⁇ g of hACE2F per reaction can be detected.
  • FIG. 2D Flow cytometry assay results for v-particles with hACE2F and mCherry.
  • FIG. 3A Flow cytometry data for the v-particles incubated with either 0 or 4.5 ⁇ g of Sb#68.
  • FIG. 3B Percentage of v-particles with fluorescence above 1000 (high fluorescence) as a function of inhibitor dose. Each Sb#68 concentration was measured in triplicate (using the same batch of v-particles).
  • Figure 4 Entrapment of v-particles by slncRNA-PP7bsxl4-hACE2F granules.
  • v-particle concentration was 0.1 % w/v.
  • Protein concentrations in imaged samples were (bottom-left) 842 nM, (top-right) 560 nM, and (bottom-right) 507 nM.
  • slncRNA concentration in imaged samples was 112.8 nM (bottom).
  • FIG. 1 Photograph of a Coomassie Brilliant Blue stained gel. Fanes 1-3 are from cells transfected with an hACE2-tdPP7 plasmid. Fanes 4-6 are from cells infected with an hACE2-tdMS2 plasmid. Fanes 7-9 are from cells infected with an hACE2-mCherry plasmid.
  • the first lane for each test (lanes 1, 4 and 7) are the wash.
  • the second lane for each test (lanes 2, 5 and 8) is the flow.
  • the third lane for each test (lanes 3, 6 and 9) is the elution from the column.
  • FIGS. 6A-6E Hairpin-containing slncRNA molecules phase separates in vitro.
  • FIG. 6A Construct diagram depicting in vitro transcription of hairpin containing slncRNA molecules used and their gelation.
  • FIG. 6B Microscopy images showing dependence of structure morphology on the number of binding sites in the slncRNA. PCP-3x results in no visible puncta, while other slncRNAs shows multiple isolated puncta and additional larger fluorescent structures.
  • FIG. 6C Violin plots of median condensate fluorescence of slncRNA-only condensates.
  • Fig. 6D Poisson function fits for the median fluorescence intensities of the slncRNA granules.
  • FIG. 6E Ko estimates calculated from the Poisson fits, showing a dependence on the number of binding sites in the slncRNA molecule.
  • FIGS. 7A-7G slncRNAs and proteins can form RNA-protein granules in vitro.
  • FIG. 7A Construct diagram depicting the suspension of tdPCP-mCherry recombinant protein together with in vitro transcribed slncRNA, resulting in synthetic RNA-protein granules.
  • FIG. 7B Microscopy images showing an overlay of the 585 nm channel (mCherry) and the 488 nm channel (Atto-488).
  • FIG. 7C Boxplots of median 585 nm (mCherry) fluorescence intensity values collected from multiple granules.
  • RNA-protein granule data in panels C,D was collected from 60 PCP-3x granules, 27 PCP-3x/MCP-3x granules, 26 PCP-4x granules, 31 PCP-4x/MCP-4x granules, 79 PCP-8x granules, and 79 PCP-14x/MCP-14x granules.
  • RNA granule data was collected from 112 PCP-3x/MCP-3x granules, 165 PCP-4x granules, 204 PCP-4x/MCP-4x granules, 121 PCP-8x granules, and 89 PCP-14x/MCP-15x granules.
  • Fig. 7E Structured illumination super resolution images of (Top) slncRNA-protein granule, and (Bottom) slncRNA-only granule. Both based on PCP-14x ⁇ MCP-15x slncRNA. Scale bar is 2 ⁇ m .
  • FIGS. 8A-8G Granule temporal dynamics are dependent on slncRNA configuration.
  • FIG. 8A Sample traces of the PCP-14x/MCP-15x slncRNA with tdPCP- mCherry SRNP granules with annotations of puncta signal. Annotations represent increasing intensity burst events (green), decreasing intensity burst events (red), and non-classified signal (blue), respectively.
  • FIG. 8B Amplitude distributions gathered from -156 signal traces in vitro.
  • FIG. 8C Boxplots depicting positive amplitude distributions for all slncRNAs.
  • FIG. 8D Matching sample traces of both slncRNA fluorescence (top) and protein fluorescence (bottom) measured from a single granule over the course of 60 minutes.
  • FIG. 8E Boxplots depicting ratio between granule protein fluorescence and mean burst amplitude.
  • Fig. 8F Boxplots depicting ratio between granule slncRNA fluorescence and mean burst amplitude.
  • FIG. 8G Boxplots depicting distributions of durations between a positive burst and a subsequent positive burst, and durations between a negative burst and a subsequent negative burst.
  • Data in panels C, E, F, G gathered from: 167 traces from PP7-3x granules, 117 traces from PP7-4x granules, 151 traces from PP7-8x granules, 71 traces from PCP-3x/MCP-3x granules, 99 traces from PCP-4x/MCP-4x granules, and 156 traces from PCP-14x/MCP-15x granules.
  • FIG. 9A-9E Synthetic phase separated droplets within bacterial cells.
  • FIG. 9A Construct diagram depicting expression of the two slncRNA cassettes used in the in vivo experiments, in the presence of tdPCP-mCherry.
  • FIG. 9B (Left) Merged DIC-585 nm image of cell expressing the PCP-24x slncRNA together with tdPCP-mCherry.
  • FIG. 9C (Left) Merged DIC-585 nm image of cell expressing the negative control RNA together with tdPCP-mCherry.
  • FIG. 12 PCP-24x granules amplitude distribution. Empirical amplitude distributions gathered from 391 traces in vivo from cells expressing the PCP-24x slncRNA together with the tdPCP-mCherry protein. Positive amplitudes (insertion events), negative amplitudes (shedding events), unclassified events are indicated in the legend.
  • FIG. 13A and 13B Fitting of amplitude data to Poisson distributions. Poisson functions fits for the amplitude distribution of insertion events assuming 1, 2, or 3 mean events (l values). MSE values represent mean squared error between the empirical distribution and the theoretical modified Poisson functions.
  • Fig. 13A Data collected from 255 PCP-4x/QCP-5x signal traces.
  • Fig. 13B Data collected from 391 PCP-24x signal traces.
  • Figures 14A-14D Image processing scheme.
  • Fig. 14A Raw microscopy image showing bacterial cells containing bright spots.
  • Fig. 14B Bright spots are identified and their position over time and space is recorded.
  • Fig. 14C The environment of each spot is classified into 3 regions, based on intensity values.
  • the brightest pixels are classified as ‘spot’ (marked in white), the darkest pixels are classified as ‘dark background’ indicating empty space, and pixels with intermediate values are classified as cell background (marked in gray).
  • Fig. 14D The mean values of the spot pixels and cell background pixels are recorded over time resulting in the spot signal (center graph) and cell signal (top graph). The spot signal is then normalized to remove photobleaching and global background effects (bottom graph).
  • FIG. 15A Identification of burst events.
  • FIG. 15A Top: simulated step signal (original signal; solid line) with added white Gaussian noise (dashed line). Bottom: noisy signal after moving average filter.
  • Fig. 15B Intensity difference distribution for the signal presented in panel A.
  • Fig. 15C Sample experimental signal overlaid with markers indicating identified segments in green, blue, and red, corresponding to positive bursts, quiescent segments, and negative bursts.
  • FIG. 16A Signal type simulations.
  • FIG. 16A Simulated constant signal (“base signal”), with photobleaching (“with exponential component”), and added noise (bottom plot).
  • FIG. 16B Amplitude distributions of burst events identified from 1000 constant signals.
  • FIG. 16C Simulated signal with slope (upper line, top plot), with photobleaching (lower line, top plot), and added noise (bottom plot).
  • FIG. 16D Amplitude distributions of burst events identified from 1000 sloped signals.
  • FIG. 16E Simulated signal with burst events (top line, upper ploy), with photobleaching (lower line, top plote), and added noise (bottom plot).
  • FIG. 16F Amplitude distributions of burst events identified from 1000 bursty signals.
  • FIG. 17A Example of different sub-frame lengths. Image is a sub-frame with length of 30 pixels. Squares corresponding to sub-frames of length 20, 14 and 10 pixels are shown.
  • Fig. 17B Ratio between cell background area to spot area (both are in number of pixels).
  • Fig. 17C Percentage of cells where the area ratio presented in (Fig. 17B) is less than one, indicating probable underestimation of the cell background.
  • Fig. 17D Ratio between spot mean intensities to cell background mean intensities (i.e., each spot is divided by its corresponding cell background). Horizontal lines represent 25 and 75 percentiles.
  • FIG. 18A Moving average span length selection.
  • Fig. 18 A Sample simulated signal used for testing. Top line of the top plot “base signal” is the underlying constant signal, whereas the lower line in the top plot (“with photobleaching”) represents the same signal with an added photobleaching component. The bottom plot describes the “with photobleaching” signal with added white Gaussian noise.
  • Fig. 18B Total number of identified events of any kind per simulated signal.
  • Fig. 18C Positive amplitude histograms of PCP-24x data analyzed using a moving average filter of 9 time points and 13 time points, as indicated in legend .
  • Fig. 18D Duration between positive events of PCP-24x data analyzed using a moving average filter of 9 time points and 13 time points.
  • FIG. 19A Schematic of the v-particle binding assay.
  • Fig. 19B depicts a schematic of the inhibitor assay as compared to the decoy assay described herein.
  • FIGs 20A-20C Optimizing v-particle synthesis and binding assay using flow cytometry.
  • Fig. 20A Increasing amounts of tdPP7-mCherry were covalently attached to carboxyl fluorescent yellow particles (bare bead), and mCherry fluorescence of FITC- positive events was measured by flow cytometry. Schematic is indicated on top of the figure. Plateau of fluorescence indicates saturation of tdPP7-mCherry attachment onto bare bead, which is observed at 0.5 tdPP7-mCherry ratio (x300,000) per 1 bead particle (or 150,000 tdPP7-mCherry per 1 bead particle).
  • V-particle synthesized with low amount of RBD [0.001 - 0.1 RBD ratio (x300,000) per 1 bead particle] or excess amount of RBD [5, 10 RBD ratio (x300,000) per 1 bead particle] shows limited or inhibited hACE2F binding
  • v-particle with bead:RBD ration of 1: 0.5 - 2 (x300,000) shows optimal binding of hACE2F. Bead without any attachment is indicated as bead only).
  • Fig. 20C Specificity of v-particle binding to hACE2F. Increasing amount of hACE2F was mixed with either v-particle or bare bead, as indicated in the legend .
  • FIG. 21A-21D Inhibition of v-particle - hACE2F binding by sybodies Sb#15, Sb#68 and GS4.
  • Fig. 21A Sybodies Sb#15 (Sbl5), Sy#68 (Sb68), and a fusion of Sbl5 and Sb68 (GS4), were prepared and used in the assay.
  • Fig. 21B Flow cytometry data for GS4. Top histogram shows fluorescence associated with no inhibitor, corresponding to maximum florescence. Bottom histogram shows fluorescence associated with bead only, or fluorescence noise level.
  • FIG. 21 C Flow cytometry data obtained from v-particle-hACE2F inhibition by Sb#15, Sb#68, and GS4. Fluorescence associated with no inhibitor is indicated. Fluorescence associated with bead only is labeled “bead only”. The molecular ratio of three components hACE2F, RBD, and inhibitor is indicated.
  • FIG. 21D Flow cytometry data obtained from v-particle-hACE2F inhibition by control proteins BSA and GST. Fluorescence associated with no protein indicated.
  • Bead only Fluorescence associated with bead only is labeled “bead only”.
  • the molecular ratio of three components; hACE2F, RBD, and protein is indicated.
  • commercial BSA and GST buffer components e.g. glycerol may have interfered with the assay.
  • FIGs 22A-22E Entrapment of v-particles by slncRNA-PP7bsxl4-hACE2F granules.
  • FIG. 22A Schematic of the hACE2F SRNP granules sequestration assay.
  • RNA containing PP7 binding sites is incubated with hACE2F proteins to form SRNP granules with high protein concentration.
  • SRNP granules attach to the v-particles via hACE2-RBD binding, serving as decoys.
  • FIG. 22B-22E Overlay of fluorescence microscopy images at 585 nm (mCherry) and 490 nm (FITC) excitation wavelengths.
  • FIG. 22B v-particles incubated with tdPP7-mCherry
  • FIG. 22C v-particles incubated with slncRNA-PP7bsxl4 - tdPP7-mCherry granules
  • FIG. 22D v-particles incubated with hACE2F
  • FIG. 22E v-particles incubated with slncRNA-PP7bsxl4 - hACE2F granules.
  • v-particle concentration was 0.1 % w/v.
  • Protein concentrations in imaged samples were (Fig. 22B, 22C) 842 nM, (Fig. 22D) 560 nM, and (Fig. 22E) 507 nM.
  • slncRNA-PP7bsxl4 concentration in imaged samples was 112.8 nM (Fig. 22C, 22E).
  • FIG. 23A Optimization of ACE2F to v-particle reaction.
  • Figure 24 Additional clusters of V-particles with ACE2F-granules showing specific binding.
  • FIGs. 25A-25E Dose response of therapeutic on the Omicron and Delta variants.
  • FIGs. 25A and 25B Confirmation that anticorona SRNP granules can be a candidate broad- spectrum therapeutic
  • FIG. 25A Granule (diamonds) and ACE2F - protein only (circles) dose responses quantified as inhibition of infection on VERO cells for delta and omicron.
  • FIG.25B Plaque images corresponding to the Omicron granule dose-response experiment as compared with a non-therapeutic control.
  • FIG. 25C Simulation of the virus priming model for a set of random parameters (k, y, a, and K v ).
  • the simulation captures the three major features of the experimental results. Namely, enhancement of infection at low therapeutic concentration, increase in IC50 and amplitude of enhancement peaks as a function of an increasing number of priming steps as observed for delta when compared to Omicron, or when comparing the granule to protein-only results.
  • the role of the granule is to effectively reduce the number of priming steps by providing a high density of ACE2F at the point of virus-granule interaction. (Dashed line) corresponds to the fixed concentration of cells used in the simulation (10 L 6), and results remain similar for different choices of (k, y, a, and K v ).
  • Figs. 25D and 25E graphically depict the degree of percent inhibition (Fig. 25D) and fold enhancement (Fig. 25E) of SARS-CoV-2 delta variant and omicron variant as a function of slncRNA concentration ( ⁇ g/ml).
  • Figure 26 graphically depict the results of a study measuring slcRNA granules (tdPP7-granules or ACE2F-granules) injected into rabbits at a lower concentration (Rabbits 40 and 41) or a higher concentration (Rabbits 42 and 43) of slncRNA.
  • Fig. 27 graphically depicts dissolution profiles from micro-needle technology.
  • Profile one top left, Fig. 27
  • Profile two bottom-left, Fig. 27
  • Profile two administers 50% of the dose on initial application with the bolus dose of the remaining material at day 30.
  • Profile two is similar to the dosing profile generated by the protocol used for the two-dose COVID-19 vaccines (i.e. Pfizer, Modema, and Astra-Zenica).
  • Profile three top-right, Fig. 27 provides a gradual initial dosing of drug from day 1 to day 25.
  • profile four bottom-right, Fig. 27
  • Profile four allows for a bolus dose of drug.
  • Profile four is a gradual dose of drug from initial administration until depletion.
  • the present invention in some embodiments, provides soluble fusion proteins comprising an extracellular domain of a human receptor or a fragment thereof and a bacteriophage coat protein, as well as synthetic microcarriers comprising a solid support conjugated to a plurality of viral proteins or fragments thereof.
  • Nucleic acid molecules and vectors encoding the soluble fusion protein, synthetic RNA-protein granules comprising a fusion protein, as well as method using the soluble fusion protein and/or the synthetic microcarriers are also provided.
  • a fusion protein comprising a fragment of a receptor and a first bacteriophage coat protein.
  • the terms “peptide”, “polypeptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues.
  • the terms “peptide”, “polypeptide” and “protein” as used herein encompass native peptides, peptidomimetics (typically including non-peptide bonds or other synthetic modifications) and the peptide analogues peptoids and semipeptoids or any combination thereof.
  • the peptides polypeptides and proteins described have modifications rendering them more stable while in the body or more capable of penetrating into cells.
  • the terms “peptide”, “polypeptide” and “protein” apply to naturally occurring amino acid polymers.
  • the terms “peptide”, “polypeptide” and “protein” apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid.
  • fusion protein refers to a single polypeptide chain that contains domains or moieties from two distinct proteins that do not appear in a single polypeptide chain in nature.
  • a fusion protein comprises a protein, such, as a human receptor or a viral protein, and a hairpin RNA binding protein, such as a phage coat protein.
  • the fusion protein is a chimeric protein.
  • the fusion protein is an artificial protein. In some embodiments, the fusion protein is not found in nature.
  • the fusion protein may be formed by the joining of two or more peptides through a peptide bond formed between the amino-terminus of one peptide and the carboxyl-terminus of another peptide.
  • the two or more peptides are joined by a linker.
  • the linker is an amino acid linker.
  • the fusion protein may be expressed as a single polypeptide fusion protein from a nucleic acid sequence encoding the single contiguous conjugate.
  • fusion proteins are created through the joining of two or more genes that originally coded for separate proteins or fragments of proteins. Recombinant fusion proteins may be created artificially by recombinant DNA technology for use in biological research or therapeutics.
  • a fusion protein can comprise a first part that is an extracellular domain of a protein, and a second part (e.g., genetically fused to the first part) that comprises a bacteriophage coat protein (e.g., the full-length protein).
  • a bacteriophage coat protein e.g., the full-length protein.
  • Methods of fusion protein generation, recombinant protein generation, recombinant DNA generation, and DNA fusion techniques are well known in the art, and any such method for making the chimeric molecules of the invention may be employed.
  • the fusion protein is soluble.
  • the fusion protein is a secreted fusion protein.
  • the fusion protein is devoid of a transmembrane domain. In some embodiments, the fusion protein comprises a signal peptide. In some embodiments, the fusion protein comprises a transmembrane domain. In some embodiments, the fusion protein is hydrophilic. In some embodiments, the fusion protein is secretable. In some embodiments, secretable is able to be secreted by a cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the mammal is human.
  • the term “receptor” refers to a protein that binds to a target molecule, e.g., its ligand, and, transduces a signal in response to that binding.
  • the term “functional fragment” when used in the context of a receptor protein refers to a fragment of the receptor that retains the ability to bind to a ligand of the receptor or any other protein to which the receptor binds, such as a viral protein.
  • a functional fragment of a human receptor is a fragment of the extracellular domain of the human receptor, such as ACE2, which can bind to a viral protein, such as the spike protein of SARS-CoV-2.
  • synthetic-RNA protein granule refers to particle comprising more than one RNA with at least three hairpins each comprising a phage coat protein binding motif, and at least one phage coat protein (having an RNA binding region that recognizes the hairpin) conjugated to a protein, such as a human receptor or a viral protein.
  • a protein such as a human receptor or a viral protein.
  • the association of the RNA and phage coat protein forms an ordered RNA/protein complex such that the RNA is primarily on the outside of the complex and the fusion protein is internalized in the granule.
  • the granules can also form, at least in part, by cross-linking of unbound hairpins via tertiary RNA interaction such as “kissing-loop”.
  • the protein and the phage coat protein are a fusion protein.
  • the fusion may comprise a tandem dimer of the phage coat protein, e.g., a tandem dimer of PP7 coat protein, where the therapeutic protein is fused to one of the tandem phage coat proteins.
  • subject refers to any animal classified as a mammal, e.g., human and non human mammals. Examples of non-human animals include dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, and etc. Unless otherwise noted, the terms “patient” or “subject” are used herein interchangeably. Preferably, the subject is human.
  • treating includes the administration of a therapeutic substance to a subject to prevent or delay the onset of the symptoms, complications, alleviating the symptoms or arresting or inhibiting further development of the disease, condition, or disorder.
  • Subjects in need of treatment include those already suffering from the disease or disorder as well as those being at risk of developing the disorder. Treatment may be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease.
  • prevention or "preventing” refers to the
  • inhibition of the development or onset of a condition e.g., a viral infection or a condition associated therewith
  • a condition e.g., a viral infection or a condition associated therewith
  • the subject may be an individual at risk of developing the condition. It is understood that prevention may not result in complete protection against onset of the symptoms associated with the condition.
  • a therapeutically effective amount of an agent refers to an amount of the agent, e.g., a synthetic RNA-protein granule, which is effective, upon single or multiple dose administration to the subject, in preventing or treating a disease or a viral infection.
  • an "at risk” individual is an individual who is at risk of developing a condition to be treated.
  • An individual “at risk” may or may not have detectable disease or condition, and may or may not have displayed detectable disease prior to the treatment of methods described herein.
  • At risk denotes that an individual has one or more so-called risk factors, which are measurable parameters that correlate with development of a disease or condition and are known in the art.
  • “At risk” may also denote that the subject does not necessarily physically have a factor which puts them at risk, e.g., immunocompromised or overweight, but will be in a situation where they may be at risk, e.g., in a crowded environment, which can lead to an increase of infection given proximity of others to the subject.
  • a length of about 1000 nanometers (nm) refers to a length of 1000 nm+- 100 nm.
  • RNA-protein granules which form an ordered complex with RNA essentially forming the outside of the granule and a therapeutic protein on the interior of the granule.
  • RNA-protein granules described herein can be used to deliver a therapeutic agent, including a prophylactic agent, to a subject.
  • the permeability of the RNA-protein granule is determined, at least in part, by the number of phage cap protein binding motifs within the RNA molecule (hairpins) and the number of respective phage coat proteins which bind to the RNA motifs.
  • the granule is formed, at least in part, by the binding of a bacteriophage coat protein to the RNA containing the protein binding motifs.
  • the RNA contains at least three hairpins comprising binding motifs recognized by phage coat proteins.
  • the bacteriophage cap protein can be fused (or otherwise conjugated, e.g., via click chemistry, such that the proteins remain functional) to a therapeutic protein.
  • the number of hairpins with protein binding sites and the number of RNA binding proteins (phage cap proteins) impacts the rate by which the therapeutic agent is released from the granule. At a minimum there are 3 hairpins.
  • the discovery of the RNA-protein granules described herein has many uses, including, but not limited to, drug delivery (both therapeutic and prophylactic) and drug screening.
  • RNA protein granules are stable such that they can be delivered to a human subject through a microneedle array, e.g., a patch containing such an array.
  • the granules can also form, at least in part, by cross-linking of unbound hairpins via tertiary RNA interaction such as “kis sing-loop”.
  • an RNA-protein granule comprises fusion proteins containing one type of therapeutic protein, e.g., fusion proteins comprising a human receptor, e.g., ACE2, or a fragment thereof, or a viral protein, e.g., a spike protein.
  • fusion proteins comprising a human receptor, e.g., ACE2, or a fragment thereof, or a viral protein, e.g., a spike protein.
  • an RNA-protein granule comprises different types of therapeutic proteins, variants of the same type of therapeutic protein, or combinations of both.
  • An RNA-protein granule is not limited in the types of fusion proteins that can be contained within the granule and may contain a diverse population of fusion proteins.
  • an RNA-protein granule may include a first fusion protein comprising a viral protein from a first virus, e.g., coronavirus, and also contain a second fusion protein comprising a viral protein from a second virus, e.g., influenza.
  • an RNA-protein granule may contain a fusion protein comprising a viral protein from a virus, e.g., coronavirus, as well as fusion proteins comprising variants of the same viral protein.
  • a fusion protein comprising a viral protein from a virus, e.g., coronavirus
  • variants may be obtained, for example, from a library containing known variants for a given virus and/or mutated versions of said viral protein to try provide further variation of the given viral protein.
  • an RNA-protein granule may comprise different fusion proteins comprising the spike protein of SAS-CoV-2 or a variant thereof, including known variants such as delta or omicron, or variants of variants created using a library having mutated versions thereof.
  • an RNA-protein granule can comprise a population of fusion proteins containing different proteins, such that the granule, in the context of a vaccine, can create a broader immune response from the subject into whom it is delivered.
  • a “therapeutic protein” includes a protein used for treating a condition, such as a viral infection, or a therapeutic that is used prophylactically.
  • therapeutic proteins that can be included in the granule described herein are receptors, e.g., human receptors that bind to a viral protein, and a viral protein, e.g., a spike protein which can be used to elicit an immune response in the subject.
  • a therapeutic protein is an antibody, e.g., an scFv.
  • the RNA is a synthetic RNA.
  • a synthetic RNA-protein granule comprises a fusion protein comprising a therapeutic protein, and a first bacteriophage coat protein, wherein the first bacteriophage coat protein is an RNA binding protein (RBP); and a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RBP RNA binding protein
  • the RNA-protein granules are cross-linked in order to make solid-particles. Such cross-linking can be achieved using click-chemistry, which should further stabilize them. Thus, in certain embodiments, any conjugation (whether of the different protein parts and/or the various RNA parts of the granule) can make similarly active particles.
  • the agent is a synthetic RNA-protein granule.
  • the granule comprises an agent.
  • the protein in the granule is an agent.
  • the granule comprises a protein that binds to the viral protein or a fragment thereof.
  • an RNA-protein (RNP) granule comprising: a fusion protein comprising a fragment of a receptor and a first bacteriophage coat protein; and a synthetic RNA molecule comprising a plurality of binding sites of the first bacteriophage coat protein.
  • the fusion protein is a fusion protein of the invention.
  • the binding sites are binding sites of the first bacteriophage coat protein.
  • the synthetic RNA comprises binding sites of the second bacteriophage coat protein.
  • the binding sites are for the first and second bacteriophage coat proteins.
  • a plurality is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19. Each possibility represents a separate embodiment of the invention. In some embodiments, the plurality is at least 17. In some embodiments, the binding sites are separated by a linker.
  • RNA-protein granules described herein are formed by the interaction of an RNA comprising hairpins and fusion proteins containing proteins, such as phage cap proteins, that contain RNA binding regions that recognize the hairpins of the RNAs.
  • ribonucleotide and the phrase “ribonucleic acid” (RNA) refer to a modified or unmodified nucleotide or polynucleotide comprising at least one ribonucleotide unit.
  • a ribonucleotide unit comprises a hydroxyl group attached to the 2' position of a ribosyl moiety that has a nitrogenous base attached in N-glycosidic linkage at the 1 position of a ribosyl moiety, and a moiety that either allows for linkage to another nucleotide or precludes linkage.
  • the RNA does not comprise a DNA base.
  • the RNA molecule is a hybrid RNA-DNA molecule.
  • RNA refers to a man-made, artificial RNA.
  • a synthetic RNA is not found in nature.
  • a synthetic RNA is purified RNA.
  • a synthetic RNA comprises a purity of at least 80, 85, 90, 95, 97, 98, 99 or 100% purity. Each possibility represents a separate embodiment of the invention.
  • a synthetic RNA is produced by a method that does not include transcription.
  • a synthetic RNA is not produced in a cell or nucleus.
  • the synthetic RNA is not polyadenylated.
  • the synthetic RNA does not comprise a 5’ cap.
  • the synthetic RNA comprises a non-natural nucleic acid base.
  • the synthetic RNA comprises thymine.
  • the synthetic RNA is a non-coding RNA. In some embodiments, the synthetic RNA does not encode a protein. In some embodiments, the synthetic RNA does not comprise an open reading frame. In some embodiments, the synthetic RNA is not a microRNA (miR). In some embodiments, the synthetic RNA is not a small interfering RNA (siRNA). In some embodiments, the synthetic RNA is not a heterologous nuclear RNA. In some embodiments, the synthetic RNA is not part of a heterologous nuclear riboprotein.
  • miR microRNA
  • siRNA small interfering RNA
  • the synthetic RNA is not a heterologous nuclear RNA. In some embodiments, the synthetic RNA is not part of a heterologous nuclear riboprotein.
  • the synthetic RNA is not any one of a microRNAs (miRNAs), small interfering RNAs (siRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), small temporal RNAs (stRNAs), antigene RNAs (agRNAs), piwi-interacting RNAs (piRNAs) or other short regulatory nucleic acid molecule.
  • miRNAs microRNAs
  • siRNAs small interfering RNAs
  • snRNAs small nuclear RNAs
  • snoRNAs small nucleolar RNAs
  • stRNAs small temporal RNAs
  • agRNAs antigene RNAs
  • piRNAs piwi-interacting RNAs
  • the synthetic RNA cannot be translated.
  • the synthetic RNA does not have a function in nature.
  • the synthetic RNA is a synthetic long non-coding RNA (slncRNA).
  • SlncRNAs are disclosed in US Patent application US20210095296 herein incorporated by reference in its entirety.
  • the synthetic RNA comprises an artificial base. In some embodiments, the synthetic RNA comprises an artificial secondary structure. In some embodiments, the synthetic RNA comprises a chemically modified backbone. Chemical modifications to the backbones of RNA molecules are well known in the art and any such modification may be used. These modifications often enhance the half-life and/or stability of the molecule. Commonly used modifications include for example 2-O-methyl modification, and phosphorodiamidate (PMO) modification.
  • PMO phosphorodiamidate
  • synthetic RNA comprises at most 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10000 nucleotides. Each possibility represents a separate embodiment of the invention.
  • the synthetic RNA is a short RNA.
  • synthetic RNA comprises at least, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, or 5000 nucleotides.
  • the synthetic RNA comprises only one binding site and is short. It will be understood by a skilled artisan that the more binding sites present in the molecule the longer the molecule will be.
  • the binding site is a canonical binding site.
  • Canonical RBP- binding sites are well known in the art and can be found for myriad RBPs.
  • the canonical binding site for PCP is uaaggaguuuauauggaaacccuua (SEQ ID NO: 15)
  • the canonical site for QCP is augcaugucuaagacagcau (SEQ ID NO: 16)
  • the canonical site for MCP is acaugaggaucacccaugu (SEQ ID NO: 17).
  • the canonical binding site for PCP is SEQ ID NO: 15.
  • the binding site comprises at least one mutation.
  • the mutation enhances binding.
  • the mutation decreases binding.
  • the binding site is a synthetic binding site.
  • the synthetic RNA is devoid of a canonical binding site.
  • the synthetic RNA-protein granule comprises an RNA, e.g., a slncRNA, comprising at least three hairpins; at least four hairpins; at least five hairpins; at least 8 hairpins; at least 10 hairpins; at least 12 hairpins; at least 14 hairpins; at least 62 hairpins; at least 18 hairpins; at least 20 hairpins; at least 22 hairpins; at least 24 hairpins; at least 26 hairpins; at least 28 hairpins; at least 30 hairpins; at least 32 hairpins; at least 34 hairpins; at least 36 hairpins; at least 38 hairpins; at least 40 hairpins; at least 42 hairpins; at least 44 hairpins; at least 46 hairpins; at least 48 hairpins; at least 50 hairpins; or no more than 50 hairpins.
  • the hairpins may contain the same motif to which a phage coat protein binds or may contain different motifs to which
  • the synthetic RNA-protein granule comprises an RNA, e.g., slncRNA, comprising 3 to 50 hairpins; 3 to 48 hairpins; 3 to 46 hairpins; 3 to 44 hairpins; 3 to 46 hairpins; 3 to 44 hairpins; 3 to 42 hairpins; 3 to 40 hairpins; 3 to 38 hairpins; 3 to 36 hairpins; 3 to 34 hairpins; 3 to 32 hairpins; 3 to 30 hairpins; 3 to 28 hairpins’ 3 to 26 hairpins;
  • RNA e.g., slncRNA
  • the hairpins are not the same sequence.
  • the hairpins may contain binding motifs that are recognized by different phage coat proteins.
  • the RNA comprises hairpins that include motifs bound by the same phage coat protein interspersed with hairpins comprising motifs bound by a second phage coat protein.
  • the hairpins contain binding motifs that are recognized by the same phage coat protein.
  • ncRNA or "non-coding RNA” as used herein designates a functional RNA molecule that is not translated into a protein.
  • IncRNA or "long non-coding RNA” is commonly used in the art and designates an nc; RNA comprising more than 200 nucleotides.
  • a “slncRNA” refers to a synthetic long non-coding RNA.
  • the synthetic RNA-protein granule may comprise a synthetic long non-coding RNA (slncRNA).
  • Synthetic long non-coding RNAs (slncRNAs) described herein are composed of non-repeat sequences in certain embodiments.
  • the slncRNA comprises non repeat sequences containing RBP binding sites.
  • slncRNA is more effective in granule formation when it contains a plurality of binding sites which are not all repeat sequences but are non-repeat sequences containing RBP binding sites.
  • binding sites examples such binding sites, as well as how to identify such binding sites, are described in US 20210095296 entitled “Synthetic Non-Coding RNAs”, as well as PCT WO 2022/070185, each of which is incorporated by reference herein.
  • slncRNA-protein granules described herein are genetically encoded platforms for the selective storage of proteins as well as a model system.
  • the slncRNA may be arranged in various formations.
  • synthetic RNA in a first group of slncRNAs (or class I slnRNAs), synthetic RNA has multiple hairpins, e.g., 3, 4, 5, 6, 7, or 8 hairpins, which are each spaced apart by a randomized sequence that does not encode for a particular structure.
  • hairpins can be spaced by a randomized sequence that does not encode for a particular structure.
  • slncRNAs used in the compositions herein have a homogeneous design which is comprised of multiple CP hairpin binding sites and non-strctured spacing regions.
  • the synthetic RNA has PCP binding sites that are each spaced by hairpin structures that do not bind PCP but may bind to other RNA binding cap proteins.
  • PCP PP7 coat protein binding each spaced by hairpins structures that do not bind PCP are described in the Examples below and include PCP-3x/MCP-3x, PCP-4x/MCP- 4x, and PCP-14x/MCP-15x.
  • slncRNAs used in the compositions herein have a hybrid design which is comprised of hairpin binding sites and additional hairpins in the spacing regions.
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by a first bacteriophage coat protein, wherein the at least three hairpins are separated by a randomized sequence that does not encode a particular protein or structure. In certain embodiments, the randomized sequences do not encode a hairpin.
  • a synthetic RNA-protein granule described herein has at least three hairpins, which will crosslink to the phage coat protein and form a gel-like condensate.
  • the granule can become more dense and more condensed.
  • the nature of the synthetic RNA protein granule is that it has a cross- linked RNA shell that encases proteins in high concentration.
  • Class I synthetic RNA protein granules for example, are semi-permeable and allow for the some of the proteins to diffuse out of the granule.
  • class II synthetic RNA protein granules are non-permeable and enclose the proteins within a gel like particle.
  • the granules release single slncRNA-protein complexes periodically. Rate of release depends on the number of hairpins or degree of cross-linking.
  • synthetic RNA protein (SNRP) granules constitute a genetically encoded and programmable controlled release particle for RNA and Protein.
  • SRNP granules further constitute a storage device for proteins and slncRNA at high concentration. As shown in the examples, SRNP granules in vivo can lead to increased cellular titer of protein due to storage capacity.
  • the examples described herein show that granules generate an effective multimerization of stored protein. Multimerization increases probability for protein to bind virus. Thus, granules decrease IC50 through the multimerization as compared with non-granulated protein at the same protein dosage. Namely, delivering the therapeutic protein in a granulated particle increases the therapeutic efficacy by reducing the IC50.
  • the synthetic RNA-protein granule may have certain permeability characteristics based on the number of hairpins and the number of phage coat proteins within the granule.
  • the granule can be semi-permeable or non-permeable.
  • the slncRNA comprises at least three hairpins each encoding an RNA binding motif recognized by the bacteriophage coat protein, wherein the at least three hairpins are each separated by a randomized sequence encoding a hairpin that does not have an encoding an RNA binding motif recognized by the bacteriophage coat protein.
  • the synthetic RNA comprises the sequence gaattcttatcgcgacatgcttaatacgactcactatagggagaaacgtttcgacattatatggaatgcgaaagtggaacgtaatgga catgaagacgattacgcttcacacggaggatgcgggaaacatgaagatcacccatgttcgcttaaccatggatagggatcacccat gttgcggtggtgcgtcaaccagagatttcatatgggaaactctgggacacgctgtatttatacatgaggatcaccatgtgtgcttaaat atgggtaagttgaccattaggcaactgtaagatgctccggttaattccagtttccagttttatatggaaacggaattaccgttgagcaaga acacgattacgggg
  • RNA-protein granules disclosed herein can be used to deliver a therapeutic at a certain desired rate.
  • the number of RNA binding motifs and the number of RNA binding coat proteins contained within the RNA-protein granule helps to determine the density of the granule such that the more dense the granule the slower the dissolution rate is of the therapeutic from the granule.
  • the granule can be prepared in such a way as to control a dose of a therapeutic agent (e.g., human receptor that binds to a viral protein) to a human subject as the dissolution rate can be controlled as necessary to achieve a desired dose over time.
  • a therapeutic agent e.g., human receptor that binds to a viral protein
  • the RNA-protein granule provides a steady state, effective dose of the therapeutic agent over 2 days, over 3 days, over 4 days, over 5 days, over 6 days, over 7 days, over 8 days, over 9 days, over 10 days, over 11 days, over 12 days, over 13 days, over 14 days, over 15 days, over 16 days, over 17 days, over 18 days, over 19 days, over 20 days, over 21 days, or over a month.
  • the dissolution rate may be such that the granule is essentially dissolved by the end of the time period.
  • the granule may provide a therapeutic agent over the course of a two-week period, where the therapeutic agent is steadily released into the human subject over the specified time period.
  • the fragment of a receptor is N-terminal to the bacteriophage coat protein. In some embodiments, the bacteriophage coat protein is N-terminal to the fragment of a receptor.
  • the granules described herein include a receptor fused to a bacteriophage coat protein (CP) (which binds to a CP RNA binding motif).
  • CP bacteriophage coat protein
  • the fusion protein comprises a fragment of a receptor.
  • a receptor is a native receptor. In some embodiments, the receptor is a naturally occurring receptor. In some embodiment, the receptor is a transmembrane receptor. In some embodiments, the receptor is a cell surface receptor. In some embodiments, the receptor is a plasma membrane receptor. In some embodiments, the receptor is a mammalian receptor. In some embodiments, the mammal is a human. In some embodiments, a receptor comprises an extracellular domain, a transmembrane domain and an intracellular domain. In some embodiments, the receptor comprises an extracellular domain that binds a target molecule. In some embodiments, the target molecule is a ligand of the receptor. In some embodiments, the ligand is a protein.
  • the fragment of a receptor comprises an extracellular domain of the receptor. In some embodiments, extracellular is outside of cell when the receptor is expressed in a cellular membrane. In some embodiments, the fragment comprises a fragment of an extracellular domain. In some embodiments, the fragment does not comprise a transmembrane domain. In some embodiments, the fragment does not comprise an intracellular domain. In some embodiments, a fragment comprises at least 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids. Each possibility represents a separate embodiment of the invention. In some embodiments, the amino acids are consecutive amino acids of the receptor sequence.
  • the fragment comprises at most 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 amino acids. Each possibility represents a separate embodiment of the invention. In some embodiments, a fragment does not comprise the entire amino acid sequence of the receptor.
  • the fragment is a functional fragment.
  • the function is target binding.
  • the target is a ligand.
  • the target is a viral protein.
  • a fragment is a fragment capable of binding to a target molecule.
  • a fragment is a fragment comprising ligand binding ability.
  • a fragment comprises a ligand binding domain.
  • a fragment consists of the extracellular domain of the receptor.
  • a fragment consists of the ligand binding domain of the receptor.
  • a receptor is a sequence with at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a native receptor. Each possibility represents a separate embodiment of the invention.
  • a receptor comprises a modified receptor. In some embodiments, the modified receptor comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid alterations. Each possibility represents a separate embodiment of the invention.
  • the fusion protein comprises a signal peptide.
  • the signal peptide is an N-terminal signal peptide.
  • the signal peptide is the signal peptide of the receptor.
  • the signal peptide is a signal peptide of a different secreted protein other than the receptor.
  • the fusion protein lacks a signal peptide.
  • the receptor is devoid of a signal peptide.
  • the fusion protein when expressed in a cell comprises a signal peptide and the signal peptide is cleaved upon secretion of the fusion protein.
  • the receptor is a receptor that binds a viral protein. In some embodiments, the receptor is a receptor that is bound by a viral protein. In some embodiments, the receptor is a receptor bound by a viral peplomer.
  • a “peplomer” is a protein projecting from the surface envelope of an enveloped virus that binds a receptor on a host cell surface and facilitates viral entry into the host cell. In some embodiments, a peplomer is a spike protein. In some embodiments, a peplomer comprises a receptor binding domain (RBD).
  • a receptor, or extracellular domain thereof, for use in the granule or fusion protein described herein, may be selected from a number of receptors known to bind a viral protein on a virus. Such proteins may be those that help to facilitate entry of the virus into the cell.
  • the receptor may be one that binds a viral protein on the surface of a virus which is a Retroviridae virus, Lentiviridae virus, Coronaviridae virus, a Picomaviridae virus, a Caliciviridae virus, a Flaviviridae virus, a Togaviridae virus, a Bomaviridae virus, a Filoviridae virus, a Paramyxoviridae virus, a Pneumoviridae virus, a Polyomaviridae virus, a Rhabdoviridae virus, an Arenaviridae virus, a Bunyaviridae virus, an Orthomyxoviridae virus, or a Deltavirus virus.
  • a virus which is a Retroviridae virus, Lentiviridae virus, Coronaviridae virus, a Picomaviridae virus, a Caliciviridae virus, a Flaviviridae virus, a Togaviridae virus
  • the receptor may be one that binds a viral protein on a virus selected from the group consisting of human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacoranovirus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Vims A6, A10, or A16), dengue virus, Ebola virus, Epstein-Barr virus (EBV), hepatitis A virus (hepatoviru)s, hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John Cu
  • Receptors that are bound by/bind to viral proteins are well known in the art and include, for example, SARS-CoV-2 binding to angiotensin converting enzyme 2 (ACE2), HIV binding to CD4, dengue virus binding to TIM-1, and influenza binding to alpha2,3- or alpha2, 6-type receptors.
  • ACE2 angiotensin converting enzyme 2
  • TIM-1 dengue virus binding to TIM-1
  • influenza binding to alpha2,3- or alpha2, 6-type receptors include, for example, SARS-CoV-2 binding to angiotensin converting enzyme 2 (ACE2)
  • ACE2 angiotensin converting enzyme 2
  • the receptor on the cell surface that binds to a viral protein is a receptor selected from ACE2, APN, DPP4, nucleolin, coxsackie and Adenovirus Receptor (CAR), KREMEN1, sialic acid (e.g., a glycoprotein comprising sialic acid), a lectin, or a glycosaminoglycan (e.g., heparan sulfate), AXL, Tyro3, Mer, DC-SIGN, DC-SIGNR, TLR3, RIG-I, MDA5, TIM-1, TIM-4, hMGL, an integrin (e.g., integrin a2b1, integrin ⁇ 6 ⁇ 1, integrin anb3, integrin anb6, integrin anb8, integrin beta-1), human mannose receptor, CD14, heat shock protein 70, heat shock protein 90, GRP78, PDGFRa, EGFR, BST/tetherin, PILRa, PDGFR
  • CAR
  • angiotensin-converting enzyme 2 serves as a receptor on the cell surface for certain coronaviruses, such as betacoronaviruses (e.g., SARS- CoV and SAR-CoV-2).
  • coronaviruses such as betacoronaviruses
  • SARS-CoV and SAR-CoV-2 bind, via the spike protein, to ACE2 in humans (Fan, J., et al. (2020). Nature, 581 (7807), 215-220; Bhatnagar, P. K., et al. (2008). Journal of pharmacy & pharmaceutical sciences., 11(2), Is.).
  • the fusion protein provided herein comprises an ACE2 receptor (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q9BYF1).
  • the fusion protein comprises an extracellular domain of the ACE2 receptor (e.g., see amino acid residues 18-740 of UniProt Accession No. Q9BYF1 or SEQ ID NO: 3), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., a spike protein) on a betacoronavirus, such as SARS-CoV-2.
  • the receptor is ACE2.
  • ACE2 comprises the amino acid sequence
  • ACE2 consists of SEQ ID NO: 1.
  • the signal peptide of ACE2 comprises MS S S S WLLLS LV A VT A A (SEQ ID NO: 2).
  • the signal peptide of ACE 2 consists of SEQ ID NO: 2.
  • the signal peptide of ACE2 comprises or consists of the first 17 amino acids of SEQ ID NO: 1.
  • the extracellular domain of ACE2 comprises or consists of amino acids 18 to 740 of SEQ ID NO: 1.
  • the extracellular domain of ACE2 comprises the amino acid sequence
  • sequence of ACE2 used in the compositions and methods disclosed herein is the amino acid sequence of SEQ ID NO: 37.
  • an extracellular domain of ACE2 is a sequence with at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 3. Each possibility represents a separate embodiment of the invention.
  • a fragment of the extracellular domain of ACE2 comprises a domain bound by the SARS-CoV-2 spike protein.
  • the domain is bound by the spike protein receptor binding domain (RBD).
  • RBD spike protein receptor binding domain
  • the fragment comprises at least one amino acid from SEQ ID NO: 1 selected from S19, Q24, T27, K31, H34, E35, E37, D38, Y41, Q42, L45, L79, M82, Y83, N90, Q325, R329, N330, K353, and G354.
  • the fragment comprises at least one amino acid from SEQ ID NO: 1 selected from S19, Q24, T27, K31, H34, E35, E37, D38, Y41, Q42, L45, L79, M82, Y83, N90, Q325, R329, N330, K353, and G354.
  • the fragment comprises from amino acid 19 to 45 of SEQ ID NO: 1. In some embodiments, the fragment comprises from amino acid 1249 to 45 of SEQ ID NO: 1. In some embodiments, the fragment comprises from amino acid 79 to 90 of SEQ ID NO: 1. In some embodiments, the fragment comprises from amino acid 325 to 330 of SEQ ID NO: 1. In some embodiments, the fragment comprises from amino acid 353 to 354 of SEQ ID NO: 1. In some embodiments, the fragment comprises from amino acid 325 to 354 of SEQ ID NO: 1.
  • Aminopeptidase N serves as a receptor on the cell surface for some viruses, such as a coronavirus.
  • alphacoronavirs binds (e.g., mediated by the spike protein of the alphacoronaviru)s to APN (CD13) in humans (Wong, A. et al. (2017). Nature communications , 8(1), 1-10.).
  • the fusion protein provided herein comprises a APN receptor (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P15144).
  • the fusion protein comprises an extracellular domain of the APN receptor (e.g., see amino acid residues 33-967 of UniProt Accession No. P15144), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., a spike protein) on an alphacoronavirus.
  • Dipeptidyl peptidase 4 serves as a receptor on the cell surface for certain viruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV).
  • MERS-CoV Middle East respiratory syndrome coronavirus
  • the fusion protein provided herein comprises a DPP4 receptor (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P27487).
  • the fusion protein comprises an extracellular domain of the DPP4 receptor (e.g., see amino acid residues 29-766 of UniProt Accession No. P27487), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., a spike protein) on a coronavirus, such as MERS-CoV.
  • Nucleolin serves as a receptor on the cell surface for certain viruses, such as respiratory syncytial virus (RSV).
  • RSV respiratory syncytial virus
  • human RSV binds (e.g., mediated by fusion protein (F protein) or glycoprotein (G protein) of the RSV virus) to nucleolin in humans (Tayyari, F., et al. (2011). Nature medicine , 77(9), 1132-1135).
  • the fusion protein provided herein comprises a nucleolin receptor (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P19338).
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., a F or G protein) on a coronavirus, such as respiratory syncytial virus (RSV).
  • a viral protein e.g., a F or G protein
  • Coxsackie and Adenovirus Receptor (CAR) proteins are receptors for a variety of adenoviruses and coxsackieviruses.
  • subgroup C adenoviruses e.g., human adenovirus types 2 or 5
  • CAR Coxsackie and Adenovirus Receptor
  • the fusion protein provided herein comprises a CAR receptor (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P78310).
  • the fusion protein comprises an extracellular domain of the CAR receptor (e.g ., see amino acid residues 20-237 of UniProt Accession No. P78310), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., a fiber protein) on a human adenovirus (e.g., human adenovirus types 2 or 5). In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on a coxsackievirus.
  • a viral protein e.g., a fiber protein
  • human adenovirus e.g., human adenovirus types 2 or 5
  • the receptor, or extracellular domain thereof binds a viral protein on a coxsackievirus.
  • KREMEN1 is a receptor on the cell surface for some viruses, such as enteroviruses (e.g., including coxsackievirus (CV)-A16 and CV-A10, which cause hand-foot-and-mouth disease; see ,e.g., Zhao, Y., et al (2020). Nature communications, 11(1), 1-8; Staring, J., et al. (2016). Cell host & microbe , 23(5), 636-643).
  • enteroviruses e.g., including coxsackievirus (CV)-A16 and CV-A10, which cause hand-foot-and-mouth disease; see ,e.g., Zhao, Y., et al (2020). Nature communications, 11(1), 1-8; Staring, J., et al. (2016). Cell host & microbe , 23(5), 636-643).
  • the receptor of the fusion protein provided herein comprises KREMEN 1 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q96MU8).
  • the fusion protein comprises an extracellular domain of KREMEN1 (e.g., see amino acid residues 21-392 of UniProt Accession No: Q96MU8), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on an enterovirus, such as coxsackievirus (CV)-A16 or CV-A10.
  • a variety of viruses are known to bind sialic acid as a receptor on glycoproteins.
  • Polyomaviruses bind via the viral VP1 capsid protein to sialic acid receptors in humans (Haley, Sheila A., et al. (2015). The American journal of pathology. 185( 8), 2246-2258.).
  • Influenza viruses, via hemagglutinin, also bind to membrane proteins with sialic acid (Weis, W., et al. (1988). Nature, 333(6112), 426-431; Wang, Q., et al. (2007). PNAS, 704(43), 16874-16879).
  • rotavirus can bind (e.g., via the VP4 viral protein) to sialic acid- containing receptors, with integrins and HSc70 acting as post- attachment receptors (Baker, M., & Prasad, B. V. (2010). Rotavirus cell entry. Cell entry by non-enveloped viruses, 121- 148).
  • the fusion protein provided herein comprises a sialic acid linked to a glycoprotein (or a fragment thereof).
  • the fusion protein comprises a sialic acid linked to an extracellular domain of a glycoprotein, or a fragment thereof.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., VP1) on a polyomavirus, such as BK polyomavirus, John Cunningham virus (JC virus), or a simian virus 40 (SV40).
  • a viral protein e.g., hemagglutinin
  • influenza A, influenza B e.g., influenza A, influenza B
  • a viral protein e.g., VP4 on a rotavirus.
  • Some viruses bind to proteins that include lectins or glycosaminoglycans.
  • Dengue virus, West Nile virus, and other members of the Flavivirus genus such as yellow fever virus and Japanese encephalitis virus recognize and bind to a diverse receptor molecules, including lectins and glycosaminoglycans (e.g., heparan sulfate) (Cruz- Oliveira, C., etal. (2015). FEMS microbiology reviews, 39(2), 155-170; Kleinert, R. D., etal. (2019). Viruses, 11(10), 960; Chu, J. J.., & Ng, M. L. (2004).
  • papilloma virus binds (e.g., via the viral protein LI) to the glycosaminoglycan heparan sulfate.
  • Hepatitis B virus (HBV) and Hepatitis D virus (HDV) can bind (e.g., via the viral S protein) to heparan sulfate, which is then transferred to a human sodium taurocholate co-transporting polypeptide (hNTCP) receptor (Watashi, K., & Wakita, T. (2015). Cold Spring Flarbor perspectives in medicine, 5(8), a02138).
  • Alphavirues s such as the Sindbis, virus can bind (e.g., via the viral E protein) to heparan sulfate as well as the laminin receptor (Byrnes, A. P., & Griffin, D. E. (1998). Journal of Virology, 72(9), 7349- 7356).
  • the receptor of the fusion protein provided herein comprises a glycosaminoglycan, such as heparan sulfate proteoglycans (Horvath, C. A., et al. (2010). Virology journal, 7(1), 1-7).
  • the receptor of the fusion protein provided herein comprises a lectin.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., glycoprotein E) on a Flavivirus, such as dengue virus, West Nile virus, Yellow fever virus, or Japanese Encephalitis.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., LI) on papilloma virus.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., S protein) on a Hepatitis B virus (HBV) or Hepatitis D virus (HDV).
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., E protein) on an alphavirus, such as the Sindbis virus or chikungunya virus.
  • Some virues s are capable of binding to several different receptors in mammalian cells.
  • Zika virus e.g., mediated by glycoprotein E of Zika viru
  • AXL i.e., Tyrosine -protein kinase receptor UFO
  • Tyro3, DC-SIGN, TLR3, RIG-I, MDA5, and TIM-1 i.e., L, etal. (2018). Viruses, 10(5), 233
  • Lassa virus can bind to multiple receptors, including AXL, Tyro3, and DC-SIGN (Lee, L, et al. (2016). Viruses, 10(5), 233).
  • Ebola virus e.g., mediated by the GP protein of the Ebola viru
  • Ebola virus can bind to the receptors TIM-1, DC-SIGN, L-SIGN, and hMGL ((Lee, L, et al. (2016). Viruses, 10(5), 233; Lee, J. E., & Saphire, E. O. (2009). Future virology, 4(6), 621-635).
  • West Nile virus binds (e.g., mediated by binding of glycoprotein E of West Nile virus to glycosaminoglycans) to primary receptors DC-SIGN, DC-SIGN-R, as well as the integrin anb3 (Chu, J.
  • Dengue virus, and other members of the Flavivirus genus recognize and bind to a diverse receptor molecules (e.g., glycosaminoglycans, such as heparan sulfate, and lectins; the adhesion molecule of dendritic cells (DC-SIGN), the mannose receptor (MR) of macrophages, TIM (e.g., TIM-1 and TIM-4) and TAM (e.g., Tyro3, Axl and Mer) families of transmembrane receptors, the lipopolysaccharide (LPS) receptor CD 14 or stress-induced proteins, such as the heat-shock proteins 70 and 90; and the ER chaperonin GRP78) (Cruz- Oliveira, C., el al.
  • a diverse receptor molecules e.g., glycosaminoglycans, such as heparan sulfate, and lectins
  • DC-SIGN dendritic cells
  • Herpesviridae family of virues s such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), and herpes zoster virus, can bind (e.g., mediated by the gB, gC, gD, or gH/gL viral proteins) to a variety of receptors, such as glycosaminoglycans, PILRa, PDGFRa, EGFR, BST/tetherin, myelin-associated glycoprotein (MAG), non-muscle myosin heavy chain (NMHC)-IIA, or integrins (e.g., a2b1, a6b1, anb3, anb6, anb8) (Vanarsdall, A.
  • HSV herpes simplex virus
  • CMV cytomegalovirus
  • VSV varicella-zoster virus
  • integrins e.g., a2b1, a
  • Epstein-barr virus can bind to MHC II (e.g., mediated by the gp42 viral protein), CD21 (e.g., mediated by the gp350 viral protein), CD35 (e.g., mediated by the gp350 and/or gp220 viral proteins), Beta-1 integrin (e.g., mediated by the BMRF-2 viral protein), anb6 integrin (e.g., mediated by the gH and/or gL viral proteins), or anb8 integrin (e.g., mediated by the gH and/or gL viral proteins; Chesnokova, L.
  • MHC II e.g., mediated by the gp42 viral protein
  • CD21 e.g., mediated by the gp350 viral protein
  • CD35 e.g., mediated by the gp350 and/or gp220 viral proteins
  • Beta-1 integrin e.g., mediated by the BMRF-2 viral
  • Rhino virus can bind to receptors such as ICAM-1 (e.g., ICAM-1 types A and B), LDLR (e.g., LDLR type A), and CDHR3 (e.g., CDHR3 Type C) (Greve, J. M., et al. (1989). Cell, 56(5), 839-847). HIV can bind (e.g., mediated by the viral protein gpl20) to CD4 with co-receptors CCR5 or CXCR4, depending on serotype (Wilen, C. B., et al. (2012). Cold Spring Harbor perspectives in medicine, 2(8), a006866).
  • ICAM-1 e.g., ICAM-1 types A and B
  • LDLR e.g., LDLR type A
  • CDHR3 e.g., CDHR3 Type C
  • HIV can bind (e.g., mediated by the viral protein gpl20) to CD4 with co-receptors CCR5 or
  • the receptor of the fusion protein provided herein comprises AXL (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g ., see UniProt Accession No. P30530).
  • the fusion protein comprises an extracellular domain of AXL (e.g., see amino acid residues 26-451 of UniProt Accession No. P30530), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus.
  • the receptor, or extracellular domain thereof binds a viral protein on a Lassa virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis virus).
  • a flavivirus e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis virus.
  • the receptor of the fusion protein provided herein comprises Tyro3 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q06418).
  • the fusion protein comprises an extracellular domain of Tyro3 (e.g., see amino acid residues 41-429 of UniProt Accession No. Q06418), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus.
  • the receptor, or extracellular domain thereof binds a viral protein on a Lassa virus.
  • the receptor of the fusion protein provided herein comprises Tyrosine-protein kinase Mer (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q12866).
  • the fusion protein comprises an extracellular domain of Mer (e.g., see amino acid residues 21-505 of UniProt Accession No. Q12866), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., west nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s.
  • the receptor of the fusion protein provided herein comprises DC-SIGN (also known as Dendritic Cell-Specific Intercellular adhesion molecule-3- Grabbing Non-integrin or CD209), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q9NNX6).
  • the fusion protein comprises an extracellular domain of DC-SIGN (e.g., see amino acid residues 59-404 of UniProt Accession No. Q9NNX6), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on a Lassa virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on an Ebola virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein (e.g., glycoprotein E) on West Nile virus.
  • a viral protein e.g., glycoprotein E
  • the receptor of the fusion protein provided herein comprises DC-SIGNR (also known as C-type lectin domain family 4 member M or CLEC4M or L- SIGN), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q9H2X3).
  • the fusion protein comprises an extracellular domain of DC-SIGN-R (e.g., see amino acid residues 71-399 of UniProt Accession No. Q9H2X3), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., glycoprotein E) on a flavivirus, such as West Nile virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on an Ebola virus.
  • a viral protein e.g., glycoprotein E
  • a flavivirus such as West Nile virus.
  • the receptor, or extracellular domain thereof binds a viral protein on an Ebola virus.
  • the receptor of the fusion protein provided herein comprises Toll-like receptor 3 (TLR3), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. 015455).
  • TLR3 Toll-like receptor 3
  • the fusion protein comprises an extracellular domain of TLR3, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus.
  • the receptor of the fusion protein provided herein comprises RIG-I (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. 095786).
  • the fusion protein comprises an extracellular domain of RIG-I, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus.
  • the receptor of the fusion protein provided herein comprises MDA5 (also known as Interferon-induced helicase C domain-containing protein 1, IFH1), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q9BYX4).
  • the fusion protein comprises an extracellular domain of MDA5, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus.
  • TIM-family proteins serve as receptors for a variety of viruses, such as Zika virus, Ebola virus, and Flaviviruses.
  • the Hepatitis A virus (HAV) may also bind TIM-1, although recent studies indicate TIM-1 may not be required for cellular entry of HAV (Das, A., et al. (2019). Journal of Virology, 93(11), e01793-18; Lee, I., et al (2016). Viruses, 10(5), 233.)
  • the receptor of the fusion protein is a TIM protein.
  • the receptor, or extracellular domain thereof binds a viral protein on a Zika virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on an Ebola virus. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s. In some embodiments, the receptor, or extracellular domain thereof, binds a viral protein on Hepatitis A.
  • a flavivirus e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru
  • the receptor, or extracellular domain thereof binds a viral protein on Hepatitis A.
  • the receptor of the fusion protein provided herein comprises TIM-1 (also known as Hepatitis A virus cellular receptor 1 or T-cell immunoglobulin mucin receptor 1), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q96D42).
  • the fusion protein comprises an extracellular domain of TIM-1 (e.g., see amino acid residues 21- 295 of UniProt Accession No. Q96D42), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises TIM-4 (also known as T-cell immunoglobulin and mucin domain-containing protein 4), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q96H15).
  • the fusion protein comprises an extracellular domain of TIM-4 (e.g., see amino acid residues 25-314 of UniProt Accession No. Q96H15), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises hMGL (also known as Hydroxymethylglutaryl-CoA lyase), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P35914).
  • the fusion protein comprises an extracellular domain of hMGL, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on an Ebola virus.
  • the receptor of the fusion protein provided herein comprises an integrin, such as integrin a2b1, integrin ⁇ 6 ⁇ 1, integrin anb3, integrin ⁇ 6 ⁇ 1 , integrin anb8, integrin beta-1, or a fragment thereof.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., glycoprotein E) on a flavivirus, such as West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis virus.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gH/gL viral proteins) on Epstein-Barr virus.
  • the receptor of the fusion protein provided herein comprises integrin a2b1 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P17301 and P05556).
  • the fusion protein comprises an extracellular domain of integrin a2b1 (e.g., see amino acid residues 30-1132 of UniProt Accession No. P17301 and amino acid residues 21-728 of UniProt Accession No. P05556), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises integrin ⁇ 6 ⁇ 1 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P23229 and P05556).
  • the fusion protein comprises an extracellular domain of integrin ⁇ 6 ⁇ 1 (e.g., see amino acid residues 24-1050 of UniProt Accession No. P23229 and amino acid residues 21-728 of UniProt Accession No. P05556), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises integrin anb3 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P23229 and P05106).
  • the fusion protein comprises an extracellular domain of integrin anb3 (e.g., see amino acid residues 42-995 of UniProt Accession No. P23229 and amino acid residues 27-718 of UniProt Accesion No. P05106), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises integrin ⁇ 6 ⁇ 1 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g ., see UniProt Accession No. P23229 and P18564).
  • the fusion protein comprises an extracellular domain of integrin ⁇ 6 ⁇ 1 (e.g., see amino acid residues 42-995 of UniProt Accession No. P23229 and amino acid residues 22-709 of UniProt Accession No. P18564), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises integrin anb8 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P23229 and P26012).
  • the fusion protein comprises an extracellular domain of integrin anb8 (e.g., see amino acid residues 42-995 of UniProt Accession No. P23229 and amino acid residues 43-684 of UniProt Accession No. P26012), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises integrin beta-1 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P05556).
  • the fusion protein comprises an extracellular domain of integrin beta-1 (e.g., see amino acid residues 21-728 of UniProt Accession No. P05556), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor of the fusion protein provided herein comprises a mannose receptor (MR, e.g., macrophage mannose receptor), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P22897).
  • the fusion protein comprises an extracellular domain of the MR receptor (e.g., see amino acid residues 19-1389 of UniProt Accession No. P22897), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis virus).
  • a flavivirus e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis virus.
  • the receptor of the fusion protein provided herein comprises CD 14 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto ( e.g ., see UniProt Accession No. P08571).
  • the fusion protein comprises an extracellular domain of CD14, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s.
  • the receptor of the fusion protein provided herein comprises heat shock protein 70 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the fusion protein comprises an extracellular domain of heat shock protein 70, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s.
  • the receptor of the fusion protein provided herein comprises heat shock protein 90 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the fusion protein comprises an extracellular domain of heat shock protein 90, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s.
  • the receptor of the fusion protein provided herein comprises GRP78 (also known as Endoplasmic reticulum chaperone BiP, 78 kDa glucose-regulated protein, or heat shock protein 70 family protein 5), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. PI 1021).
  • the fusion protein comprises an extracellular domain of GRP78, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a flavivirus (e.g., West Nile virus, dengue virus, yellow fever virus, or Japanese encephalitis viru)s.
  • the receptor of the fusion protein provided herein comprises platelet-derived growth factor receptor alpha (PDGFRa) (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g ., see UniProt Accession No. P16234).
  • the fusion protein comprises an extracellular domain of PDGFRa (e.g., see amino acid residues 24-528 of UniProt Accession No. P16234), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises epidermal growth factor receptor (EGFR), a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P00533).
  • the fusion protein comprises an extracellular domain of EGFR (e.g., see amino acid residues 25-645 of UniProt Accession No. P00533), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises Bone marrow stromal antigen 2 (BST/tetherin) (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q10589).
  • the fusion protein comprises an extracellular domain of BST/tetherin (e.g., see amino acid residues 49-161 of UniProt Accession No. Q10589), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises Paired immunoglobulin-like type 2 receptor alpha (PILR ⁇ ), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q9UKJ1).
  • the fusion protein comprises an extracellular domain of PILRa (e.g., see amino acid residues 20-197 of UniProt Accession No. Q9UKJ1), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises Platelet-derived growth factor receptor alpha (PDGFRa) (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q8AXC8).
  • the fusion protein comprises an extracellular domain of PDGFRa, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises myelin-associated glycoprotein (MAG) (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P20916).
  • the fusion protein comprises an extracellular domain of MAG (e.g., see amino acid residues 20-516 of UniProt Accession No. P20916), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises non-muscle myosin heavy chain (NMMHC)-IIA (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P35579).
  • the fusion protein comprises an extracellular domain of NMMHC-IIA, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gB, gC, gD, or gH/gL viral proteins) on a Herpesviridae virus, such as herpes simplex virus (HSV), cytomegalovirus (CMV), varicella-zoster virus (VSV), or herpes zoster virus.
  • a viral protein e.g., gB, gC, gD, or gH/gL viral proteins
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • herpes zoster virus herpes zoster virus
  • the receptor of the fusion protein provided herein comprises HLA Class II (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the fusion protein comprises an extracellular domain of HLA Class II, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gH/gL viral proteins) on Epstein-barr virus.
  • the receptor of the fusion protein provided herein comprises CD21 (also known as Complement receptor type 2 or CR2), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P20023).
  • the fusion protein comprises an extracellular domain of CD21 (e.g., see amino acid residues 21-971 of UniProt Accession No. P20023), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gH/gL viral proteins) on Epstein-barr virus.
  • the receptor of the fusion protein provided herein comprises CD35 (also known as Complement receptor type 1 or CR1), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P17927).
  • the fusion protein comprises an extracellular domain of CD35 (e.g., see amino acid residues 42-1971 of UniProt Accession No. P17927), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gH/gL viral proteins) on Epstein-barr virus.
  • the receptor of the fusion protein provided herein comprises ICAM-1 (Intercellular adhesion molecule 1), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P05362).
  • the fusion protein comprises an extracellular domain of ICAM-1 (e.g., see amino acid residues 28-480 of UniProt Accession No. P05362), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a rhinovirus.
  • the receptor of the fusion protein provided herein comprises LDLR (also known as Sortilin-related receptor or SORL1), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. Q92673).
  • the fusion protein comprises an extracellular domain of LDLR, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a rhinovirus.
  • the receptor of the fusion protein provided herein comprises CDHR3 (Cadherin-related family member 3), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g ., see UniProt Accession No. Q6ZTQ4).
  • the fusion protein comprises an extracellular domain of CDHR3 (e.g., see amino acid residues 20-713 of UniProt Accession No. Q6ZTQ4), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein on a rhinovirus.
  • the receptor of the fusion protein provided herein comprises CD4 (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P01730).
  • the fusion protein comprises an extracellular domain of CD4 (e.g., see amino acid residues 26-396 of UniProt Accession No. P01730), or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gpl20) on HIV.
  • the receptor of the fusion protein provided herein comprises CCR5 (also known as C-C chemokine receptor type 5), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P51681).
  • the fusion protein comprises an extracellular domain of CCR5, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gpl20) on HIV.
  • the receptor of the fusion protein provided herein comprises CXCR4 (also known as C-X-C chemokine receptor type 4), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P61073).
  • the fusion protein comprises an extracellular domain of CXCR4, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., gpl20) on HIV.
  • the receptor of the fusion protein provided herein comprises sodium taurocholate co-transporting polypeptide (NTCP) (or a fragment thereof) or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g ., see UniProt Accession No. Q14973).
  • the fusion protein comprises an extracellular domain of hNTCP , or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., S protein) on a Hepatitis B virus (HBV) or Hepatitis D virus (HDV).
  • the receptor of the fusion protein provided herein comprises a laminin receptor (also known as LamR or 40S ribosomal protein SA), a fragment thereof, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto (e.g., see UniProt Accession No. P08865).
  • the fusion protein comprises an extracellular domain of the laminin receptor, or a sequence having at least 80, 85, 90, 92, 95, 97, 99 or 100% identity thereto.
  • the receptor, or extracellular domain thereof binds a viral protein (e.g., Eprotein) on an alphavirus, such as the Sindbis virus or chikungunya virus.
  • a viral protein e.g., Eprotein
  • the receptor is a poorly expressed receptor. In some embodiments, the receptor is a difficult to express receptor. In some embodiments, poorly expressed is difficult to express. In some embodiments, poorly expresses in poorly expressed from cells in culture. In some embodiments, poorly expressed is poorly expressed as an exogenous protein. In some embodiments, poorly expressed is follow exogenous expression in a cell in culture. In some embodiments, the cell is culture is human cell. In some embodiments, the cell in culture is a cell of a cell line. In some embodiments, the cell is a HEK cell. In some embodiments, the HEK cell is a HEK293 cell. In some embodiments, the HEK293 cell is a HEK293F cell.
  • exogenous expression examples include, but are not limited to infection, transfection, transduction, viral infection, lipofection, electroporation and direct alteration of a cell’s genome.
  • exogenous expression is transfection.
  • exogenous expression is viral infection.
  • the poorly expressed receptor is the receptor not fused to the first bacteriophage coat protein. In some embodiments, the poorly expressed receptor is the receptor devoid of the first bacteriophage coat protein. In some embodiments, the poorly expressed receptor is a poorly expressed fragment of the receptor. In some embodiments, the fragment of the receptor is poorly expressed. In some embodiments, the fragment of the receptor not fused to the first bacteriophage is poorly expressed.
  • poorly expressed is not expressed. In some embodiments, not expressed is not detectably expressed. In some embodiments, not expressed is not expressed above background levels. In some embodiments, poorly expressed comprises a low titer. In some embodiments, low titer is low titer in media from cell. In some embodiments, the cells are culture cells. In some embodiments, the cells are human cells. In some embodiments, the cells are cells at confluence. In some embodiments, confluence comprises at least 70, 75, 80, 85, 90, 92, 95, 97 or 99% capacity of the container containing the cells. Each possibility represents a separate embodiment of the invention.
  • low titer comprises a concentration of less than 5, 4, 3, 2, 1, 0.95, 0.9, 0.85, 0.8, 0.75 or 0.7 mg per ml. Each possibility represents a separate embodiment of the invention. In some embodiments, low titer comprises a concentration of less than 1 mg per ml. In some embodiments, the concentration is concentration in media. In some embodiments, the media is culture media. In some embodiments, the media is media from cells.
  • low titer is after purification from media. In some embodiments, low titer is after isolation from media. In some embodiments, purification is affinity purification. In some embodiments, the fusion protein comprises a tag. In some embodiments, the tag is a purification tag. In some embodiments, the tag is an affinity tag. In some embodiments, the fusion protein is isolated by binding the tag. Methods of purification/isolation such as column purification, affinity purification and the like are well known in the art and any such method may be used. In some embodiments, the tag is a His tag. In some embodiments, the tag is a 6x His tag. In some embodiments, the His tag is purified using Ni (nickel)-coated beads.
  • an RNA-protein granule comprises a viral protein, such as a spike protein of SARS-CoV-2 or an envelope protein of influenza.
  • An RNA-protein granule can comprise a fusion protein comprising a viral protein and a bacteriophage coat protein or other phage hairpin, RNA binding protein.
  • the viral protein is expressed on the surface of a virus such that delivery of the protein to a human subject results in an immune response, i.e., can be used as a vaccine.
  • the viral protein is a spike protein of the virus.
  • the viral protein is an envelope protein of the virus.
  • the RNA-protein granule may contain fusion proteins comprising a hairpin RNA- binding protein (e.g., a phage coat protein) and a first viral protein, including variants of said protein.
  • the RNA-protein granule comprises viral proteins (including variants thereof) from one or more additional viruses, e.g., fusion proteins comprising the SARS-CoV-2 spike protein, and variants and fragments thereof, and fusion proteins comprising an envelope protein from an influenza virus, and variants and functional fragments thereof.
  • an RNA-protein granule may contain antigens to multiple types of viruses.
  • RNA- protein granules comprising fragments of viral proteins.
  • Variants of a viral protein may be included in the RNA-protein granule.
  • the viral protein can be obtained a library of variants of that protein.
  • the library could contain the spike proteins of the original Wuhan strain, alpha, beta, gamma, delta, mu, iota, omicron, ba2, etc, but also, in certain embodiments, contain various combinations of the mutations observed in those spikes.
  • Any viral protein can be used so long as the protein is exposed on the surface of the virus.
  • viruses from which such viral proteins can be used in the methods and compositions disclosed herein include, but are not limited to, a human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacorano virus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Virus A6, A10, or A16), dengue virus, Ebola virus, Epstein-Barr virus (EBV), hepatitis A virus (hepatovirus), hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus,
  • a viral protein included in an RNA-protein granule disclosed herein is a spike protein.
  • a spike protein is a viral protein that projects from the surface of enveloped viruses, such as coronaviruses, orthomyxoviruses (e.g., influenza virus), paramyxoviruses, rhabdoviruses, filoviruses, bunyaviruses, arenaviruses, and retroviruses (e.g., human immunodeficiency virus (HIV)).
  • coronaviruses e.g., orthomyxoviruses (e.g., influenza virus), paramyxoviruses, rhabdoviruses, filoviruses, bunyaviruses, arenaviruses, and retroviruses (e.g., human immunodeficiency virus (HIV)).
  • orthomyxoviruses e.g., influenza virus
  • paramyxoviruses e.g., rhabdoviruse
  • viral envelope proteins e.g., spike proteins and peplomers
  • amino acid sequences can be readily accessed by one of ordinary skill in the art via public internet databases, such as those provided by the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/), UniProtKB (https://www.uniprot.org/), or European Molecular Biology Laboratory (EMBL) - European Bioinformatic Institute (https://www.ebi.ac.uk/) .
  • EMBL European Molecular Biology Laboratory
  • spike proteins that can be included in RNA-protein granules disclosed herein are provided in Table 1.
  • the viral protein is a spike protein selected from Table 1, or a variant or fragment thereof.
  • the viral protein is a polypeptide arising from post-translational (proteolytic) cleavage of a spike protein set forth in Table 1.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to an amino acid sequence of any one of the spike proteins set forth in Table 1, or a variant or fragment thereof.
  • RNA-protein granule comprising a fusion protein comprising a viral protein as set forth in Table 1, or a variant or fragment thereof, and a first bacteriophage coat protein, wherein the first bacteriophage coat protein is an RNA binding protein (RBP); and a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • RBP RNA binding protein
  • viral proteins include surface proteins on orthomyxoviruses (e.g., a neuraminidase protein or a hemagglutinin protein on influenza viruses) or surface proteins found on retroviruses (e.g., a gp41 protein or a gpl20 protein on HIV).
  • orthomyxoviruses e.g., a neuraminidase protein or a hemagglutinin protein on influenza viruses
  • retroviruses e.g., a gp41 protein or a gpl20 protein on HIV
  • the viral protein used in the methods and compositions described herein is a neuraminidase (e.g., as found in influenza viruses), or a variant or fragment thereof.
  • the neuraminidase family of proteins in influenza virus A has at least 11 different subtypes. Examples of proteins belonging to the neuraminidase family of proteins in influenza viruses can be found, for example, at EMBL-EBI InterPro Accession No. IPR033654 or IPR001860.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a viral neuraminidase protein, or a functional variant or fragment thereof.
  • the viral protein used in the methods and compositions described herein is a hemagglutinin (e.g., as found in influenza viruses), or a variant or fragment thereof.
  • the hemagglutinin family of influenza virus A has at least 18 different subtypes. Examples of proteins belonging to the hemagglutinin family of proteins in influenza virus A or influenza virus B can be found, for example, at EMBL-EBI InterPro Accession No. IPR001364. Examples of proteins belonging to the hemagglutinin family in influenza virus C can be found, for example, at EMBL-EBI InterPro Accession No. IPR014831.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a hemagglutinin protein, or a functional variant or fragment thereof.
  • the viral protein used in the methods and compositions described herein is gp41 (e.g., as found in HIV), or a variant or fragment thereof.
  • proteins belonging to the GP141 family of proteins in HIV can be found, for example, at EMBL-EBI InterPro Accession No. IPR000328.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a gp41 protein, or a functional variant or fragment thereof.
  • the viral protein used in the methods and compositions described herein is gpl20 (e.g., as found in HIV), or a variant or fragment thereof.
  • proteins belonging to the GP141 family of proteins in HIV can be found, for example, at EMBL-EBI InterPro Accession No. IPR000777.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a gpl20 protein, or a functional variant or fragment thereof.
  • the viral protein is an envelope protein that can be an antigenic fragment, or a variant thereof.
  • the viral protein is an envelope protein, or a fragment thereof, from a virus selected from a coronavirus, an orthomyxovirus (e.g., an influenza virus), a paramyxovirus, a rhabdovirus, a filovirus, a bunyavirus, an arenavirus, or a retrovirus (e.g., human immunodeficiency virus (HIV)).
  • a coronavirus an orthomyxovirus (e.g., an influenza virus), a paramyxovirus, a rhabdovirus, a filovirus, a bunyavirus, an arenavirus, or a retrovirus (e.g., human immunodeficiency virus (HIV)).
  • an orthomyxovirus e.g., an influenza virus
  • paramyxovirus e.g., a paramyxovirus
  • a rhabdovirus e.
  • the viral protein has at least 80, 85, 90, 92, 95, 97, 99 or 100% identity to a viral envelope protein (e.g., from a coronavirus, an orthomyxovirus (e.g., an influenza viru)s, a paramyxovirus, a rhabdovirus, a filovirus, a bunyavirus, an arenavirus, or a retro virus (e.g., human immunodeficiency virus (HIV))), for fragment thereof.
  • a viral envelope protein e.g., from a coronavirus, an orthomyxovirus (e.g., an influenza viru)s, a paramyxovirus, a rhabdovirus, a filovirus, a bunyavirus, an arenavirus, or a retro virus (e.g., human immunodeficiency virus (HIV))
  • HIV human immunodeficiency virus
  • RNA-protein granule described herein comprises a fusion protein comprising a therapeutic protein, such as a human receptor from a cell surface or a viral protein, and a RNA binding protein (RBP) that binds to hairpins, which are found in the RNA of the granule.
  • a therapeutic protein such as a human receptor from a cell surface or a viral protein
  • RBP RNA binding protein
  • the RBP that binds to hairpins is a cap protein from phage.
  • Bacteriophages are well known in the art and include for example PP7, MS2, GA, and Qbeta. Each bacteriophage has a known coat protein whose sequence is publicly available.
  • the Bacteriophage or phage is selected from PP7, MS2, GA, and Qbeta (Q ⁇ ).
  • the phage is PP7.
  • the phage is MS2.
  • the phage is not MS2.
  • the phage is GA
  • the phage is Qp.
  • the Bacteriophage or phage is selected from PP7, GA and Qp.
  • PP7 is Pseudomonas phage PP7.
  • MS2 is Escherichia virus MS2.
  • Q ⁇ is Escherichia virus Qbeta.
  • the PP7 coat protein is PCP.
  • the MS2 coat protein is MCP.
  • the Q ⁇ coat protein is QCP.
  • the coat protein is a capsid coat protein.
  • the coat protein is a capsid protein.
  • the coat protein is the PP7 coat protein.
  • the PP7 coat protein comprises the amino acid sequence S KTIVLS V GE ATRTLTEIQS T ADRQIFEEKV GPLV GRLRLT AS LRQN G AKT A YR VN LKLD Q AD V VDC S TS VC GELPKVR YTQ VW S HD VTIV AN S TE AS RKS LYDLTKS LV V QATSEDLVVNLVPLGR (SEQ ID NO: 21).
  • the PP7 coat protein consists of SEQ ID NO: 21.
  • the coat protein comprises at least one mutation that decreases binding to another coat protein.
  • the mutation decreases binding of a dimer of the coat protein to another dimer of the coat protein.
  • the PP7 is PP7delFG.
  • PP7delFG comprise reduced binding.
  • PP7delFG comprises the amino acid sequence S KTIVLS V GE ATRTLTEIQS T ADRQIFEEKV GPLV GRLRLT AS LRQN G AKT A YR VN LKLD Q AD V VDS GLPKVR YTQ VW S HD VTIV AN S TEAS RKS LYDLTKS LV AT S Q VE DLVVNLVPLGR (SEQ ID NO: 4).
  • the PP7delFG coat protein consists of SEQ ID NO: 4. In some embodiments, the PP7delFG coat protein comprises SEQ ID NO: 4. In some embodiments, the PP7 coat protein comprises an N-terminal di-amino acid LA. In some embodiments, the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 21. Each possibility represents a separate embodiment of the invention. In some embodiments, the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 4. Each possibility represents a separate embodiment of the invention.
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 21. Each possibility represents a separate embodiment of the invention. In some embodiments, the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 4. Each possibility represents a separate embodiment of the invention.
  • the coat protein is the MS2 coat protein.
  • the MS2 coat protein comprises the amino acid sequence: MAS NFTQFVLVDNGGTGD VT V APS NF AN G V AE WIS S NS RS Q A YKVTCS VRQS S A QNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAM QGLLKDGNPIPS AIA AN S GIY (SEQ ID NO:39), or a functional variant or fragment thereof (e.g., a variant or fragment of the coat protein that is capable of binding a corresponding nucleotide binding site, such as a binding site on a slncRNA).
  • MS2 coat protein is also described in Uniprot Accession No. P03612.
  • the MS2 coat protein comprises SEQ ID NO: 39.
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 39.
  • Each possibility represents a separate embodiment of the invention.
  • Each possibility represents a separate embodiment of the invention.
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 39.
  • Each possibility represents a separate embodiment of the invention.
  • the coat protein is the GA coat protein.
  • the GA coat protein comprises the amino acid sequence: M ATLRS F VLVDN GGT GN VT V VP V S N AN G V AEWLS NN S RS Q A YR VT AS YR AS G A DKRKYAIKLEVPKIVTQVVNGVELPGSAWKAYASIDLTIPIFAATDDVTVISKSLAG LFKVGNPIAEAISSQSGFYA (SEQ ID NO:40), or a functional variant or fragment thereof (e.g., a variant or fragment of the coat protein that is capable of binding a corresponding nucleotide binding site, such as a binding site on a slncRNA).
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 40. Each possibility represents a separate embodiment of the invention. Each possibility represents a separate embodiment of the invention. In some embodiments, the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 40. Each possibility represents a separate embodiment of the invention.
  • the coat protein is the Qbeta (Q ⁇ ) coat protein.
  • the Qbeta (Q ⁇ ) coat protein comprises the amino acid sequence: M AKLET VTLGNIGKDGKQTLVLNPRGVNPTN GVAS LS Q AGA VPALEKRVTV S VS QPS RNRKN YKV Q VKIQNPT ACT AN GS CDPS VTRQ A Y AD VTFS FTQ Y S TDEERAF V RTELAALLASPLLIDAIDQLNPAY (SEQ ID NO:42), or a functional variant or fragment thereof (e.g., a variant or fragment of the coat protein that is capable of binding a corresponding nucleotide binding site, such as a binding site on a slncRNA).
  • the Qbeta (Q ⁇ ) coat protein is also described in Uniprot Accession No. P03615.
  • the Qbeta (Q ⁇ ) coat protein comprises SEQ ID NO: 42.
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 42.
  • Each possibility represents a separate embodiment of the invention.
  • Each possibility represents a separate embodiment of the invention.
  • the bacteriophage coat protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 42.
  • Each possibility represents a separate embodiment of the invention.
  • the phage RNA binding protein is a lambda (l) phage RNA- hairpin binding protein.
  • the lambda phage protein is lambda antitermination protein N.
  • the lambda (l) protein comprises the amino acid sequence:
  • Lambda N protein is also described in Uniprot Accession No. P03045.
  • the lambda (l) protein comprises SEQ ID NO: 41.
  • the bacteriophage protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% homology to SEQ ID NO: 41.
  • Each possibility represents a separate embodiment of the invention.
  • Each possibility represents a separate embodiment of the invention.
  • the bacteriophage protein comprises at least 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100% identity to SEQ ID NO: 41.
  • Each possibility represents a separate embodiment of the invention.
  • the fusion protein further comprises a second bacteriophage coat protein.
  • the fusion protein may comprise different RNA binding proteins, e.g., PP7 and MS2.
  • a bacteriophage coat protein is a plurality of bacteriophage coat proteins, e.g., two or more RNA binding proteins that are the same or different from one another but each recognize.
  • a bacteriophage coat protein is two bacteriophage coat proteins.
  • the first and second bacteriophage coat proteins are the same protein.
  • the same proteins comprise the same amino acid sequence.
  • the same proteins comprise at least 80, 85, 90, 95, 97, 99 or 100% identity to each other.
  • the first and second bacteriophage coat proteins are different proteins.
  • the fusion protein comprises a tandem repeat of the bacteriophage coat protein.
  • a tandem repeat is a tandem dimer.
  • a tandem repeat are identical repeats of the bacteriophage coat protein.
  • the dimer is a homodimer. In some embodiments, the dimer is a heterodimer. It is known in the art that bacteriophage coat proteins naturally form dimers and in particular homodimers.
  • the therapeutic agent of the fusion protein is an antibody or antigen binding fragment thereof.
  • the antibody or antigen binding fragment thereof is to the viral protein or a fragment thereof.
  • the term "antibody” refers to a polypeptide or group of polypeptides that include at least one binding domain that is formed from the folding of polypeptide chains having three-dimensional binding spaces with internal surface shapes and charge distributions complementary to the features of an antigenic determinant of an antigen.
  • An antibody typically has a tetrameric form, comprising two identical pairs of polypeptide chains, each pair having one "light” and one "heavy” chain. The variable regions of each light/heavy chain pair form an antibody binding site.
  • An antibody may be oligoclonal, polyclonal, monoclonal, chimeric, camelised, CDR-grafted, multi- specific, bi-specific, catalytic, humanized, fully human, anti- idiotypic and antibodies that can be labeled in soluble or bound form as well as fragments, including epitope-binding fragments, variants or derivatives thereof, either alone or in combination with other amino acid sequences.
  • An antibody may be from any species.
  • the term antibody also includes binding fragments, including, but not limited to Fv, Fab, Fab', F(ab')2 single stranded antibody (svFC), dimeric variable region (Diabody) and disulphide-linked variable region (dsFv).
  • antibodies include immunoglobulin molecules and immunologically active fragments of immunoglobulin molecules, i.e., molecules that contain an antigen binding site.
  • Antibody fragments may or may not be fused to another immunoglobulin domain including but not limited to, an Fc region or fragment thereof.
  • Fc region or fragment thereof The skilled artisan will further appreciate that other fusion products may be generated including but not limited to, scFv- Fc fusions, variable region (e.g., VL and VH) ⁇ Fc fusions and scFv- scFv-Fc fusions.
  • Immunoglobulin molecules can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2) or subclass.
  • the RNA-protein granule further comprises a thereapeutic agent which is a small molecule.
  • a small molecule may be conjugated to the RNA-binding protein in addition to, or instead of, a human receptor or a viral protein.
  • the small molecule is designed to bind to the viral protein or a fragment thereof.
  • the agent is a synthetic peptide.
  • the synthetic peptide is designed to bind to the viral protein or a fragment thereof.
  • the granule comprises an antibody, small molecule or synthetic peptide. In some embodiments, the granule comprises a natural peptide. In some embodiments, the natural peptide binds to the viral protein or a fragment thereof. In some embodiments, the granule comprises an antibody, small molecule, synthetic peptide or natural peptide. In some embodiments, the granule is a granule of the invention.
  • the fusion protein further comprises a detectable moiety.
  • the detectable moiety is a detectable protein domain.
  • the term "moiety”, as used herein, relates to a part of a molecule that may include either whole functional groups or parts of functional groups as substructures.
  • the term “moiety” further means part of a molecule that exhibits a particular set of chemical and/or pharmacologic characteristics which are similar to the corresponding molecule.
  • the detectable moiety is a fluorescent moiety.
  • the fluorescent moiety is a fluorescent protein domain.
  • a fluorescent moiety is a fluorophore.
  • fluorescent moieties include, but are not limited to GFP, RFP, YFP, mCherry, CY3, CY5, CY7, Atto, and luciferase.
  • the fluorescent moiety is mCherry.
  • mCherry comprises the amino acid sequence MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTK GGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVV TVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKG EIKQRLKLKD GGH YD AE VKTT YKAKKP V QLPG A YN VNIKLDIT S HNED YTIVEQ Y ERAEGRHSTGGMDELYK (SEQ ID NO: 5).
  • mCherry consists of SEQ ID NO: 5. In some embodiments, mCherry in a fusion protein lacks an N-terminal methionine. In some embodiments, an mCherry lacking a methionine comprises the amino acid sequence
  • an mCherry lacking a methionine consists of SEQ ID NO: 6.
  • the fusion protein further comprises a tag.
  • the tag is an affinity tag.
  • the tag is a purification tag.
  • the tag is a His tag.
  • the His tag is a 6x His tag.
  • a 6x His tag consists of the amino acid sequence HHHHHH (SEQ ID NO: 7).
  • the tag is a C-terminal tag.
  • the tag is an N-terminal tag.
  • the fusion protein further comprises a linker.
  • the linker is an amino acid linker.
  • the linker is a peptide bond.
  • the linker comprises at least 0, 1, 2, or 3 amino acids. Each possibility represents a separate embodiment of the invention.
  • the linker comprises at least 3 amino acids.
  • the linker comprises 3 amino acids.
  • the linker consists of 3 amino acids.
  • the linker comprises at most 30, 25, 20, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, or 3 amino acids. Each possibility represents a separate embodiment of the invention.
  • the linker comprises at most 5 amino acids.
  • the linker comprises 5 amino acids.
  • the linker comprises between 3-5 amino acids. In some embodiments, the linker is a flexible linker. In some embodiments, the linker is a rigid linker. In some embodiments, the linker comprises the amino acid sequence ADP. In some embodiments, the linker consists of the amino acid sequence ADP. In some embodiments, the linker comprises the amino acid sequence PPVAT (SEQ ID NO: 8). In some embodiments, the linker consists of SEQ ID NO: 8.
  • the fragment of a receptor is N-terminal to the detectable moiety.
  • the bacteriophage coat protein is N-terminal to detectable moiety.
  • the detectable moiety is N-terminal to the fragment of the receptor.
  • the detectable moiety is N-terminal to the bacteriophage coat protein.
  • the N-terminus of the fusion protein is the fragment of a receptor.
  • the C-terminus of the fusion protein is the bacteriophage coat protein.
  • the C-terminus of the fusion protein is the tag.
  • the detectable moiety is between the fragment of a receptor and the bacteriophage coat protein. In some embodiments, the fragment of a receptor is between the detectable moiety and the bacteriophage coat protein. In some embodiments, the bacteriophage coat protein is between the fragment of a receptor and the detectable moiety. In some embodiments, the fusion protein comprises, from N-terminus to C-terminus, the fragment of a receptor, and the bacteriophage coat protein. In some embodiments, the fusion protein comprises, from N-terminus to C-terminus, the fragment of a receptor, the detectable moiety and the bacteriophage coat protein. In some embodiments, the fusion protein comprises, from N-terminus to C-terminus, the fragment of a receptor, the detectable moiety, the bacteriophage coat protein and the tag.
  • the fragment of a receptor and the bacteriophage coat protein are separated by a linker. In some embodiments, the fragment of a receptor and the detectable moiety are separated by a linker. In some embodiments, the fragment of a receptor and the tag are separated by a linker. In some embodiments, the bacteriophage coat protein and the detectable moiety are separated by a linker. In some embodiments, the bacteriophage coat protein and the tag are separated by a linker. In some embodiments, detectable moiety and the tag are separated by a linker. In some embodiments, the first bacteriophage coat protein and the second bacteriophage coat protein are separated by a linker.
  • the tandem repeats are separated by a linker.
  • the fusion protein consists of, from N-terminus to C-terminus, the fragment of a receptor, a linker and the bacteriophage coat protein. In some embodiments, the fusion protein consists of, from N- terminus to C-terminus, the fragment of a receptor, a linker the detectable moiety, a linker and the bacteriophage coat protein. In some embodiments, the fusion protein consists of, from N-terminus to C-terminus, the fragment of a receptor, a linker, the detectable moiety, a linker, the bacteriophage coat protein and the tag.
  • the receptor is human ACE2, the detectable moiety is mCherry, and the bacteriophage coat protein is a tandem repeat of two copies of a PP7 capsid.
  • the receptor is human ACE2, the detectable moiety is mCherry, the bacteriophage coat protein is a tandem repeat of two copies of a PP7 capsid and the tag is a His-tag.
  • the fusion protein comprises the amino acid sequence
  • the fusion protein comprises the amino acid sequence MSS S S WLLLS LV A VT A AQS TIEEQ AKTFLD KFNHE AEDLF Y QS S LAS WN YNTNITE EN V QNMNN AGDKW S AFLKEQS TLAQM YPLQEIQNLT VKLQLQ ALQQN GS S VLS E DKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAW ESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDY S RGQLIED VEHTFEEIKPLYEHLH AY VR AKLMN A YPS YIS PIGCLP AHLLGDMW GR FWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGF WENSLLTDPGNVQKAVCHPTAWDLGKGDFRIL
  • nucleic acid molecule encoding a fusion protein of the invention.
  • a vector comprising a nucleic acid molecule of the invention.
  • the nucleic acid molecule comprises an open reading frame.
  • the open reading frame encodes the fusion protein of the invention.
  • the open reading frame is operatively linked to at least one regulatory element.
  • the regulatory element is configured to induce expression of the open reading frame.
  • expression is transcription of the open reading frame.
  • expression is translation of the open reading frame.
  • expression of a nucleic acid molecule may refer to transcription of the nucleic acid fragment (e.g., transcription resulting in mRNA or other functional RNA) and/or translation of RNA into a precursor or mature protein (polypeptide).
  • an open reading frame within a cell is well known to one skilled in the art. It can be carried out by, among many methods, transfection, viral infection, or direct alteration of the cell’s genome.
  • the open reading frame is in an expression vector such as plasmid or viral vector.
  • expression comprises introducing a nucleic acid molecule or a vector into a cell.
  • a vector nucleic acid sequence generally contains at least an origin of replication for propagation in a cell and optionally additional elements, such as a heterologous polynucleotide sequence, expression control element (e.g., a promoter, enhancer), selectable marker (e.g., antibiotic resistance), poly-Adenine sequence.
  • expression control element e.g., a promoter, enhancer
  • selectable marker e.g., antibiotic resistance
  • poly-Adenine sequence e.g., antibiotic resistance
  • the vector is an expression vector.
  • the vector may be a DNA plasmid delivered via non-viral methods or via viral methods.
  • the viral vector may be a retroviral vector, a herpes viral vector, an adenoviral vector, an adeno-associated viral vector or a poxviral vector.
  • the promoters may be active in mammalian cells.
  • the promoters may be a viral promoter.
  • the open reading frame is operably linked to a promoter.
  • operably linked is intended to mean that the nucleotide sequence of interest is linked to the regulatory element or elements in a manner that allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).
  • an open reading frame is a coding region.
  • the vector is introduced into the cell by standard methods including electroporation (e.g., as described in From et al. Proc. Natl. Acad. Sci. USA 82, 5824 (1985)), Heat shock, infection by viral vectors, high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (Klein et al. Nature 327. 70-73 (1987)), and/or the like.
  • promoter refers to a group of transcriptional control modules that are clustered around the initiation site for an RNA polymerase i.e., RNA polymerase II. Promoters are composed of discrete functional modules, each consisting of approximately 7-30 bp of DNA, and containing one or more recognition sites for transcriptional activator or repressor proteins.
  • nucleic acid sequences are transcribed by RNA polymerase II (RNAP II and Pol II).
  • RNAP II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA.
  • mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1 ( ⁇ ), pGL3, pZeoSV2( ⁇ ), pSecTag2, pDisplay, pEF/myc/cyto, pCMV/myc/cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK- RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.
  • expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses are used by the present invention.
  • SV40 vectors include pSVT7 and pMT2.
  • vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p205.
  • exemplary vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo- 5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
  • recombinant viral vectors which offer advantages such as lateral infection and targeting specificity, are used for in vivo expression.
  • lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells.
  • the result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles.
  • viral vectors are produced that are unable to spread laterally. In one embodiment, this characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.
  • plant expression vectors are used.
  • the expression of a polypeptide coding sequence is driven by a number of promoters.
  • viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al. Nature 310:511-514 (1984)], or the coat protein promoter to TMV [Takamatsu et al. EMBO J. 3:1671-1680 (1984); and Brogli et al.
  • constructs are introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach [Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 (1988)].
  • Other expression systems such as insects and mammalian host cell systems, which are well known in the art, can also be used by the present invention.
  • the expression construct of the present invention can also include sequences engineered to optimize stability, production, purification, yield or activity of the expressed polypeptide.
  • the expression vector is configured to express the fusion protein in a target cell. In some embodiments, the expression vector is configured to express the fusion protein from a target cell. In some embodiments, the expression vector is configured to express the fusion protein in a target cell and have it secreted therefrom. In some embodiments, the target cell is a mammalian cell. In some embodiments, the target cell is a human cell.
  • the open reading frame or a portion thereof is codon optimized.
  • codon optimized is optimized for expression in a target cell. Codon optimization is well known in the art and any method of optimization may be employed. Optimization generally alters the nucleotide sequence so as to match parameters found in the target cell, such as dinucleotide bias, codon usage bias, rate of translation and many others. Optimization generally does not alter the amino acids sequence produced by the open reading frame.
  • codon optimized is optimized for expression in mammalian cells frame.
  • codon optimized is optimized for expression in human cells.
  • the sequence encoding the fragment of a receptor is codon optimized.
  • the sequence encoding the bacteriophage coat protein is optimized. In some embodiments, the sequence encoding the detectable moiety is optimized. In some embodiments, the first bacteriophage coat protein is encoded by a first nucleotide sequence. In some embodiments, the second bacteriophage coat protein is encoded by a second nucleotide sequence. In some embodiments, the first sequence and the second sequence are different nucleotide sequences. In some embodiments, the first and second bacteriophage coat proteins are the same amino acid sequence and the first and second nucleotide sequences are different nucleotide sequences.
  • mCherry is encoded by the nucleotide sequence gtgagcaagggcgaggaggataacatggccatcatcaaggagttcatgcgcttcaaggtgcacatggagggctccgtgaacgg ccacgagttcgagatcgagggcgagggcgagggccgcccctacgagggcacccagaccgccaagctgaaggtgaccaagg gtgg gtgg gtggccccctgcctgggacatcctgtccctcagttcatgtacggctccaaggcctactgtgtgaagcaccccgccgacatcccccctcagttcatgtacggctccaaggcctacgtgtgaagcaccccgcc
  • tandem repeat of PP7delFG is encoded by ctagcctccaaaaccatcgttctttcggtcggcgaggctactcgcactctgactgagatccagtccaccgcagaccgtcagatcttc gaagagaaggtcgggcctctggtgggtcggctgcgcctcacggcttcgctcgtcaaaacggagccaagaccgcgtatcgcgtc aacctaaactggatcaggcggacgtcgttgattccggacttccgaaagtgcgctacactcaggtatggtcgcacgacgtgacaat cgttgcgaatagcaccgaggcctcgcgcaaatcgttgcgaatagcaccgaggcctcgcgcaaatc
  • human ACE2 extracellular domain is encoded by atgtcaagctcttcctggctccttctcagccttgttgctgtaactgctgctcagtccaccattgaggaacaggccaagacatttttggac aagtttaaccacgaagccgaagacctgttctatcaaagttcacttgcttcttggaattataacaccaatattactgaagagaatgtccaa aacatgaataatgctggggacaaatggtctgcctttttaaaggaacagtccacacttgcccaaatgtatccactacaagaaattcaga atctcacagtcaagcttctgcaggctctttcagcaggaatgggtcttcagcaagaaattcaga at
  • codon optimized human ACE2 extracellular domain is encoded by atgtctagctctagttggctgctcctgtctttggtcgctgtcacggccgcgcagtctactatcgaagaacaggccaaacattcctgg ataagttcaaccacgaggcggaagaccttttctatcaaagcagtttggcgagttggaattataatacaaatatcacagaggaaaatgt ccagaacatgaacaacgctggagacaagtggagtgcttttctgaaggaacagagtacgttggcccaaatgtaccccctgcaagaa attcaaaacctgacggttaaactccaattgcaagcactccaacaaaatggttcaagtgtgctcac
  • the fusion protein is encoded by atgtctagctctagttggctgctcctgtctttggtcgctgtcacggccgcgcagtctactatcgaagaacaggccaaacattcctgg ataagttcaaccacgaggcggaagaccttttctatcaaagcagtttggcgagttggaattataatacaaatatcacagaggaaaatgt ccagaacatgaacaacgctggagacaagtggagtgcttttctgaaggaacagagtacgttggcccaaatgtaccccctgcaagaa attcaaaacctgacggttaaactccaattgcaagcactccaacaaaatggttcaagtgtgctcagcgaggaggagga
  • Another aspect of the disclosure is a portion of the human ACE2 protein which can be used to treat or prevent SARS-CoV-2 infection.
  • the ACE2 protein binds to the spike protein of SARS-CoV-2 and can be used to neutralize the virus.
  • amino acid and nucleic acid sequences of the human ACE2 protein are provided herein in the Sequence Table.
  • an isolated protein encoding soluble human ACE2 wherein the protein comprises the amino acid sequence set forth in SEQ ID NO: 37.
  • the isolated ACE2 protein can be used to treat a human subject infected with SARS- CoV-2 or a human subject who is at risk of being infected with SARS-CoV-2.
  • the ACE2 protein e.g., the protein of SEQ ID NO: 37, or a functional fragment thereof, is administered to the human subject in need.
  • the ACE2 protein e.g., the protein of SEQ ID NO: 37, is used in a method to prevent coronavirus disease in a human subject.
  • the ACE2 protein can be delivered to the human subject in a manner consistent with the therapy.
  • the ACE2 protein is administered to the human subject intradermally.
  • Intradermal delivery can be achieved using a microneedle array.
  • a microneedle array comprising a therapeutic amount of ACE2 protein is incorporated into a patch which is affixed on the skin of a human subject in need.
  • the ACE2 protein, or a functional fragment thereof can also be fused to a phage coat protein and included in an RNA-protein granule complex.
  • a method of expression a fragment of a receptor in a cell comprising: a. providing an expression vector comprising a coding region, wherein said coding region encodes a fusion protein comprising the fragment of a receptor and bacteriophage coat protein; and b. introducing the expression vector into the cell; thereby expression a fragment of a receptor in a cell.
  • the fusion protein is a fusion protein of the invention.
  • the expression vector is an expression vector of the invention.
  • the expression vector comprises a nucleic acid molecule of the invention.
  • the cell is a target cell.
  • the expression is in the cell.
  • the expression is from the cell.
  • the expression is secretion from the cell.
  • the expression comprises secretion from the cell.
  • the expression vector is configured to express a protein encoded by the coding region.
  • the expression vector is configured to induce expression a protein encoded by the coding region.
  • the expression vector is suitable to induce expression of the coding region.
  • expression is expression in the cell.
  • induce expression is induce expression in the cell.
  • the method is a method of expressing a difficult to expresses fragment of a receptor. In some embodiments, the method is a method of expressing a poorly expressed fragment of a receptor. In some embodiments, a difficult to express fragment of a receptor is a fragment of a receptor that when expressed not as the fusion protein is expressed at less than 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, 15, 10 5 or 1% of the expression when expressed as a fusion protein. Each possibility represents a separate embodiment of the invention.
  • a difficult to express fragment of a receptor is a fragment of a receptor that when expressed not as the fusion protein is expressed at less than 50% of the expression when expressed as a fusion protein. In some embodiments, a difficult to express fragment of a receptor is a fragment of a receptor that when expressed not as the fusion protein is expressed at less than 10% of the expression when expressed as a fusion protein. In some embodiments, a difficult to express fragment of a receptor is a fragment of a receptor that when expressed not as the fusion protein is not detectably expressed. In some embodiments, detectably expressed is expressed above background. Detection of protein and quantification of protein expression is well known in the art and may be performed by any known method.
  • the detecting is immunoblotting. In some embodiments, the detecting is ELISA. In some embodiments, the detecting is nanodrop quantification. In some embodiments, the detecting is A600 quantification. In some embodiments, the nanodrop quantification is A600 quantification. In some embodiments, A600 is absorbance at 600.
  • a synthetic microcarrier comprising a support conjugated to a plurality of viral proteins or fragments thereof.
  • the support is a solid support. In some embodiments, the support is a semisolid support. In some embodiments, the support is a surface. In some embodiments, the support is a bead. In some embodiments, the support is an artificial support. In some embodiments, the support is a man-made support. In some embodiments, the bead is a microbead. In some embodiments, the support is a capture support. In some embodiments, the bead is a magnetic bead. In some embodiments, the bead is a paramagnetic bead. In some embodiments, the bead is a polystyrene bead. In some embodiments, the bead is organic. In some embodiments, the bead is non-organic. In some embodiments, the support is a fluorescent support. In some embodiments, the support is auto-fluorescent.
  • the beads used herein may be of any convenient size and fabricated from any number of known materials.
  • Example of such materials include: inorganics, natural polymers, and synthetic polymers. Specific examples of these materials include: cellulose, cellulose derivatives, acrylic resins, glass, silica gels, polystyrene, gelatin, polyvinyl pyrrolidone, co polymers of vinyl and acrylamide, polystyrene cross-linked with divinylbenzene or the like, polyacrylamides, latex gels, polystyrene, dextran, rubber, silicon, plastics, nitrocellulose, natural sponges, silica gels, control pore glass, metals, cross-linked dextrans (e.g., SephadexTM) agarose gel (SepharoseTM), and other solid phase supports known to those of skill in the art.
  • the bead is a polystyrene bead.
  • the support comprises a diameter of between 0.25 and 1, 0.3 and 1, 0.35 and 1, 0.4 and 1, 0.45 and 1, 0.5 and 1, 0.55 and 1, 0.6 and 1, 0.65 and 1, 0.7 and 1, 0.75 and 1, 0.8 and 1, 0.9 and 1, and 0.92 and 1 micron.
  • the solid support comprises a diameter of between 0.25 and 1 micron.
  • the solid support comprises a diameter of between 0.5 and 1 micron.
  • the solid support comprises a diameter of between 0.7 and 1 micron.
  • the solid support comprises a diameter of between 0.9 and 1 micron.
  • the support is detectable by microscopy. In some embodiments, the support is detectable by flow cytometry.
  • the viral protein is expressed on a viral surface. In some embodiments, the viral protein is expressed on surface of virions. In some embodiments, the viral protein is a structural protein. In some embodiments, the viral protein is a peplomer. In some embodiments, the fragment is a functional fragment. In some embodiments, the fragment is capable of protein binding. In some embodiments, the fragment is capable of binding a target protein. In some embodiments, the target protein is a non-viral protein. In some embodiments, the viral protein is a host protein. In some embodiments, the target protein is a receptor. In some embodiments, the receptor is the receptor used for viral entry.
  • the fragment comprises a receptor binding domain (RBD).
  • viral protein is a SARS-CoV-2 protein.
  • the viral protein is a spike protein.
  • the SARS-CoV-2 spike protein RBD comprises the amino acid sequence
  • MFVFLVLLPLV S QRV QPTES IVRFPNITNLCPF GE VFN ATRF AS V Y A WNRKRIS N C V AD Y S VLYN S AS FS TFKC Y G V S PTKLNDLCFTN V Y ADS FVIRGDE VRQIAPGQTGK IADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY Q AGS TPCNG VEGFNC YFPLQS Y GF QPTN G V GY QP YRV V VLS FELLH AP AT VCGPK KSTNLVKNKCVNF (SEQ ID NO: 19).
  • the SARS-CoV-2 spike protein RBD consists of SEQ ID NO: 19.
  • the SARS-CoV-2 spike protein RBD is encoded by atgttcgtgtttctggtgctgctgcctctggtgtccagccagcgggtgcagcccaccgaatccatcgtgcggttccccaatatcacca atctgtgccccttcggcgaggtgttcaatgccaccagattcgcctctgtgtacgcctggaaccggaagcggatcagcaattgcgtg gccgactactccgtgctgtacaactccgccagcttcagcaccttcaagtgctacggcgtgtcccctaccaagctgaacgacctgtgtgctcacaaac
  • the plurality of viral protein or fragments thereof is at least 1,000, 5,000, 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000, 150,000, 200,000, 250,000, 300,000 or 350,000 viral proteins or fragments thereof. Each possibility represents a separate embodiment of the invention. In some embodiments, the plurality of viral protein or fragments thereof is at least 10,000 viral proteins or fragments thereof. In some embodiments, the plurality of viral protein or fragments thereof is at least 100,000 viral proteins or fragments thereof.
  • the support comprises free functional groups.
  • a functional group is a reactive group.
  • the viral proteins or fragments thereof are conjugated to the free functional groups.
  • the function groups are carboxyl groups.
  • carboxyl groups are carboxylic acid groups.
  • the viral proteins or fragments thereof are conjugated to the support by a carbodiimide crosslinking reaction.
  • the term “functional group” refers to a molecule or a moiety within a molecule that can undergo a characteristic molecular reaction when reacted with a specific reactant.
  • Functional groups are well known in the art broad categories of functional groups include hydrocarbon functional groups (including alkane, alkene, alkyne and benzene), halogen functional groups (halide, fluoride, chloride, bromide and iodide), oxygen functional groups (hydroxyl, carbonyl, aldehyde, haloformyl, carbonate ester, carboxylate, carboxyl, carboalkyoxy, hydroperoxyl, peroxy, ether, hemiacetal, hemiketal, acetal, ketal, orthoester, methylendioxy, orthocarbonate ester, carboxylic anhydride), nitrogen function groups (amide, amine, ammonium, imine, imide, azide, diazene, cyanate, isocynate, nitrate
  • the microcarriers are for use in testing an inhibitor of virus binding.
  • the fusion proteins are for use in tested an inhibitor of receptor binding.
  • the fusion proteins are for use in tested an inhibitor of virus binding.
  • the microcarriers are for use in place of live virus.
  • the microcarriers are for use as a noninfectious virus stand-in.
  • RNA-protein granules disclosed herein can be used for treatment or prevention of a disease, including an infectious disease.
  • included in the invention is a method of treating a human subject infected with a virus or at risk of being infected with a given virus.
  • An RNA-protein granule comprising a fusion protein comprising a human receptor that binds to a viral protein can be used as an inhibitor - blocking the interaction of the viral protein with endogenous receptors in the human subject.
  • ACE2 or a functional fragment thereof, can be administered in an RNA- protein granule described herein for treatment of a SAR-CoV-2 infection, where the ACE2 protein in the RNA-protein granule binds to the virus in the human subject and prevents the virus from binding to cells for further infection.
  • viruses that can be targeted using the compositions and methods disclosed herein - either for treatment or prophylactically - include, but are not limited to, Retro viridae virus, Lentiviridae virus, Coronaviridae virus, a Picornaviridae virus, a Caliciviridae virus, a Flaviviridae virus, a Togaviridae virus, a Bomaviridae virus, a Filo viridae virus, a Paramyxo viridae virus, a Pneumo viridae virus, a Polyomaviridae virus, a Rhabdo viridae virus, an Arenaviridae virus, a Bunyaviridae virus, an Orthomyxo viridae virus, or a Deltavirus virus.
  • the receptor may be one that binds a viral protein on a virus selected from the group consisting of human adenovirus (e.g., human Adenovirus serotypes 2 or 5), BK polyomavirus, Alphacoronavirus, Betacorano virus, Chikungunya virus, Coxsackievirus (e.g., Coxsackie Virus A6, A10, or A16), dengue virus, Ebola virus, Epstein-Barr virus (EBV), hepatitis A virus (hepatovirus), hepatitis B virus (hepadnaviridae), hepatitis C virus, herpes simplex virus, herpes zoster virus, human cytomegalovirus, human immunodeficiency virus (HIV), human papillomavirus, influenza A virus, influenza B virus, Japanese Encephalitis virus, Lassa virus, Middle East respiratory syndrome -related coronavirus (MERS), norovirus, John Cunningham virus (human aden
  • the invention also provides a method for preventing a viral infection in a human subject, where the human subject is at risk of being exposed to said virus.
  • the invention also includes a vaccine, whereby the RNA-protein granule comprises a viral protein, a variant of the viral protein, and/or a fragment of the viral protein that is suitable to elicit an immune response from the subject.
  • RNA-protein granules used as a vaccine can include combinations of viral proteins, from the same virus type, e.g., SARS-CoV-2, or from different viruses, e.g., SARS-CoV-2 and influenza.
  • an RNA-protein granule comprises two, three, four, five, or more different types of viral proteins form different viruses.
  • variants of the viral protein may be included in the RNA-protein granule.
  • Variants include those identified and known in the art, e.g., the delta and omicron variants of SARS-CoV-2, as well as variants that can be created in a library directed at introducing mutations into the viral protein.
  • an RNA-protein granule comprises viral protein variants obtained from a library designed to mutate given positions within the viral protein.
  • an RNA-protein granule comprises 10, 100, 500, 1000, or thousands of variants of a given viral protein.
  • compositions disclosed herein can be used to develop a broad- spectrum vaccine against a virus, such as a coronavirus, that can be delivered to a human subject, for example via microneedle.
  • a broad spectrum vaccine is based on RNA-protein granules described herein, where granules display a library of viral proteins, e.g., spike proteins, from a virus of interest, such as SARS-CoV-2.
  • the library of viral proteins, e.g., spike proteins is computationally designed to generate thousands of mutations, with an end goal of generating essentially all possible mutations.
  • the versions of the spike protein used in the fusion proteins of the RNA-protein granules would include various mutaitons in the 10 relevant epitopes associated with antibody binding.
  • generating a library of -10,000 spike variants containing known spike variants and different variations anticipating mutations that can come and providing a therapeutic or prophylactic that is inclusive of variants - even before they occur. This is done using computational biology and protein folding tools known in the art, which can predict relatively well which mutations will be deleterious, and which are more likely to be stable.
  • the library of spike proteins is expressed and heterogeneous fusion proteins are prepared, each containing different combinations of the mutant spikes. This can then be used to generate a much broader antibody profile, which provides broad spectrum protection and provides panvariant antiviral agents.
  • RNA-protein granules can comprise a spike protein from a virus, such that the protein is used as a vaccine where the human patient’s immune system produces antibodies to the viral protein.
  • delivery of the spike protein could avoid reliance on smaller regions that may become obsolete as variants emerge.
  • the technology described herein can be used to provide a broad-spectrum vaccine that can be delivered to a human subject in need thereof, e.g., to be delivered via microneedles.
  • the method includes administering a therapeutically effective amount of a synthetic RNA-protein granule to the human subject in need thereof, wherein the synthetic RNA-protein granule comprises a fusion protein comprising an extracellular domain of a human receptor, e.g., a receptor that binds to a viral protein, or a functional fragment thereof, and a first bacteriophage coat protein, wherein the a first bacteriophage is an RNA binding protein (RBP); and a synthetic RNA molecule comprising a plurality of binding sites of said first bacteriophage coat protein.
  • a synthetic RNA-protein granule comprises a fusion protein comprising an extracellular domain of a human receptor, e.g., a receptor that binds to a viral protein, or a functional fragment thereof, and a first bacteriophage coat protein, wherein the a first bacteriophage is an RNA binding protein (RBP); and a synthetic RNA molecule comprising a plurality of binding
  • RNA-protein granule examples include, but are not limited to, ACE2, APN, AXL, BST/tetherin, CCR5, CD4, CD14, CD21, CD35, CDHR3, Coxsackie and Adenovirus Receptor (CAR), CXCR4, DC-SIGN, DC-SIGNR, DPP4, EGFR, a glycosaminoglycan, GRP78, heat shock protein 70, heat shock protein 90, hMGL, human mannose receptor, ICAM-1, an integrin, KREMEN1, LamR, LDLR, lectin, MAG, MDA5, Mer, NMMHC-IIA, NTCP, nucleolin, PDGFRa, PDGFRa, PILRa, RIG-I, a sialic acid receptor, TIM-1, TIM-4, TLR3, and Tyro3.
  • the fusion protein may also comprise an alternative therapeutic agent, such as an antibody or scFv.
  • RNA-protein granules disclosed herein can be admixed with a pharmaceutically acceptable carrier or excipient to form a pharmaceutical composition.
  • pharmaceutically acceptable carrier or excipient is meant a non-toxic solid, semisolid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type (see also Handbook of Pharmaceutical Excipients 6ed. 2010, Published by the Pharmaceutical Press).
  • RNA-protein granules disclosed herein or the pharmaceutical composition comprising said RNA-protein granules may be administered, for example, orally, parenterally, such as subcutaneously, intravenously, intramuscularly, intraperitoneally, intrathecally, transdermally, transmucosally, subdurally, locally or topically via iontopheresis, sublingually, by inhalation spray, aerosol or rectally and the like in dosage unit formulations optionally comprising conventional pharmaceutically acceptable carriers or excipients.
  • RNA-protein granules and proteins described herein are administered to the human subject intranasally.
  • pharmaceutical liquid formulations comprising an RNA-protein granule or a protein as disclosed herein, which is suitable for intranasal administration, e.g., a nasal spray, to a human subject in need thereof.
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises an RNA-protein granule or a protein as disclosed herein, saline, fluticasone, triamcinolone, oxymetazoline, and PEG.
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises sodium chloride, glycerin, citric acid, and aloe vera.
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises benzalkonium chloride, carboxymethylcellulose sodium, dextrose, edetate disodium, sodium hydroxide, microcrystalline cellulose, Tween 80, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises citric acid monohydrate, sodium citrate dihydrate, sodium chloride, Tween 80, glycerin, menthol, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises glycerol, ethanol, menthol, eucalyptus oil, potassium iodide, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for intranasal administration comprises potassium iodide, hydroxyethyl cellulose, sodium citrate dihydrate, citric acid anhydrous, menthol, glycerol, and water (e.g., purified water).
  • RNA-protein granules or proteins described herein are administered to the human subject orally, e.g., as a throat spray.
  • pharmaceutical liquid formulations comprising an RNA-protein granule or a protein as disclosed herein, which are suitable for administration to the throat, e.g., a throat spray, of a human subject in need thereof.
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, alcohol, saccharin sodium, PEG, glycerin, menthol, phenol, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, zinc gluconate, glycerin, PEG, peppermint oil, saccharin sodium, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, potassium iodate, glycerol, propanediol, peppermint oil, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, potassium iodide, glycerol, propylene glycol, mentholum, potassium iodate, Tween 80, and water (e.g., purified water).
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, sodium chloride, zinc gluconate, glycerin (vegetable), citric acid, and peppermint.
  • the pharmaceutical liquid formulation suitable for administration to the throat comprises an RNA-protein granule or a protein as disclosed herein, citric acid monohydrate, sodium citrate dihydrate, sucralose, potassium iodide, glycerine, peppermint, menthol, and water (e.g., purified water).
  • a microneedle -based therapeutic drug delivery system can be used for delivery of a protein or an RNA-protein granule (e.g., ACE2P-SRNP granules) to a human subject.
  • a protein or an RNA-protein granule e.g., ACE2P-SRNP granules
  • various microneedle-based therapeutic drug delivery systems were evaluated herein (see, e.g., Example 7) to determine the optimal mechanism for the administration of ACE2P- SRNP granules. The primary consideration in doing so was to develop a therapeutic system that can complement the global vaccine effort and address challenges that were identified as a result of issues arising with recent vaccine administration and the rapid emergence of more infectious (delta) and potentially "escape" (omicron) variants.
  • Microneedle delivery can confer several advantages for delivery of therapeutics comprising RNA and proteins - for example, the microneedle meshwork can trap protein and RNA molecules and the tight mesh size keeps protein in solid form to control release rate and maintain stability. Proteins are released through matrix defects and dosing amounts increase as hydrogel degrades. In turn, protein particles gradually free up, dissolve and diffuse out of the microneedle meshwork. Microneedle technology and fabrication techniques have previously been described in the art, as further described, for example, in U.S. Patent No.
  • the protein or RNA-protein granule is administered to a subject (e.g., a human subject) using a microneedle array.
  • a subject e.g., a human subject
  • microneedle refers to microscopic structures that are capable of piercing the stratum comeum, and, optionally, underlying epidermal layers, to facilitate the transdermal delivery of therapeutic agents (e.g., RNA and/or protein).
  • microstmctures can include needle or needle-like structures as well as other structures capable of piercing the stratum corneum (e.g., sharp, tapered-, conical- or bevel-tipped structures, microblades, blunt-projections or arrow-head shaped structures).
  • the microneedles are arranged into a microneedle array.
  • array refers to the medical devices that include a plurality of microneedles to facilitate the transdermal delivery of therapeutic agents. Arrays of microneedles can be arranged on microneedle patches.
  • any type of microneedle may be used and a RNA and/or protein of the invention (e.g., a protein or an RNA-protein granule) may be applied to the microneedle(s) in a suitable manner, according to the specific application.
  • Microneedles are typically categorized as drug-coated microneedles, dissolving microneedles, hollow microneedles, solid microneedles, and hydrogel-forming microneedles.
  • the microneedle is a drug-coated microneedle.
  • the protein or RNA-protein granule is administered transdermally to a subject by using a drug-coated microneedle or an array of drug-coated microneedles.
  • the microneedle or the microneedle array can be coated with a composition comprising the therapeutic agent (e.g., protein or RNA-protein granule).
  • the microneedle or the microneedle array is coated by dipping the microneedle or the microneedle array into a formulation comprising the therapeutic agent (e.g., protein or RNA-protein granule) and subsequently drying the coating. This process may be carried out once or repeatedly.
  • the microneedle or the microneedle array may be coated by spraying it with a formulation comprising the therapeutic agent (e.g., protein or RNA-protein granule) and subsequently drying the coating.
  • the process may be carried out once or multiple times.
  • the coating solution is an aqueous solution comprising the therapeutic agent (e.g., protein or RNA-protein granule) and optionally further pharmaceutically acceptable ingredients.
  • the coating solution may comprise a surfactant, a stabilizer and/or a thickening agent.
  • exemplary surfactants include Lutrol F-68 NF, Tween 20, Poloxamer 188 and Quil-A.
  • stabilizers include trehalose, sucrose, glucose, inulin, and dextrans.
  • Thickening agents include, for example, carboxymethylcellulose sodium salt (CMC), methylcellulose, sucrose, hyaluronic acid, sodium alginate, polyvinylpyrrolidone (PVP), glycerol, polyethylene glycol (PEG), PLGA, alginic acid, xanthan gum, gum ghatti, karaya gum, poly[di(carboxylatophenoxy)phosphazene], or a combination thereof (e.g., PEG and PGLA).
  • CMC carboxymethylcellulose sodium salt
  • PVP polyvinylpyrrolidone
  • PEG polyethylene glycol
  • PLGA alginic acid
  • xanthan gum ghatti
  • karaya gum poly[di(carboxylatophenoxy)phosphazene]
  • PEG and PGLA poly[di(carboxylato
  • the microneedle comprises a pharmaceutical formulation comprising a composition described herein, e.g., a synthetic RNA-protein granule or ACE2 protein, and PEG. In one embodiment, the microneedle comprises a pharmaceutical formulation comprising a composition described herein, e.g., a synthetic RNA-protein granule or ACE2 protein, and PGLA.
  • the microneedle may comprise a pharmaceutical formulation which is a hydrogel.
  • the microneedles are created by mold or 3D print prior to coating a formulation comprising the therapeutic agent (e.g., protein or RNA-protein granule).
  • the microneedle is one that is not removed from the patient after dosing the patient. The dissolution process of the microneedles may allow the needles and patch to slowly dissolve into the blood stream. Accordingly, in some embodiments, there is nothing (e.g., no patch or no microneedles) to remove after the drug is depleted.
  • the microneedle is a dissolving microneedle.
  • the protein or RNA-protein granule is administered transdermally to a subject by using a dissolving microneedle or an array of dissolving microneedles.
  • the dissolving microneedle as used herein comprises material that dissolves upon contact with the skin of a subject.
  • the dissolving microneedle or an array of dissolving microneedles encapsulate the therapeutic agent (e.g., protein or RNA-protein granule, which is released upon microneedle dissolution.
  • a dissolving microneedle is produced by using a mold, into which a solution comprising the therapeutic agent (e.g., protein or RNA-protein granule) is cast and allowed to dry.
  • a solution comprising the therapeutic agent e.g., protein or RNA-protein granule
  • such solution is an aqueous solution comprising the RNA and/or protein and, optionally, an additional pharmaceutical ingredient, such as one selected from the group consisting of CMC, chondroitin sulfate, dextran, dextrin, PVP, PVA, PLGA, fibroin and a sugar (e.g., trehalose, sucrose, maltose, or glucose).
  • the solution comprising the therapeutic agent e.g., protein or RNA-protein granule
  • the solution comprising the therapeutic agent is not cast in a mold, but drawn into filaments that solidify in position.
  • the microneedle is a hollow microneedle.
  • the protein or RNA-protein granule is administered transdermally to a subject by using a hollow microneedle or an array of hollow microneedles (e.g., comprising an outer core that is capable of dissolving).
  • a hollow microneedle represents a microinjection device comprising a cavity, through which the therapeutic agent (e.g., protein or RNA-protein granule) is administered.
  • the hollow microneedle is filled with a formulation comprising the therapeutic agent (e.g., protein or RNA-protein granule).
  • Hollow microneedles can be composed of a variety of materials, such glass microneedles, polymer microneedles or metal microneedles.
  • the hollow microneedles can be made, for example, with pre-made cavities, 3D printing, or the therapeutic agent can be formulated with needle coating as template.
  • the microneedle comprises a polymer (e.g., PGLA or PEG). Polymer-based microneedles may be advantageous given they can dissolve within the patient.
  • the microneedle comprising a composition described herein is made of a substance, e.g., a polymer such as PGLA or PEG, that dissolves upon application, e.g., as a patch, to a human subject.
  • a substance e.g., a polymer such as PGLA or PEG
  • the microneedle is a solid microneedle.
  • the protein or RNA-protein granule is administered transdermally to a subject by using a solid microneedle or an array of solid microneedles.
  • the basic principle therein is that the skin surface (e.g., the stratum comeum) is penetrated by the microneedle(s), which generates a channel through which the therapeutic agent (e.g., protein or RNA-protein granule) can be delivered.
  • the target skin at the administration site is pre-treated with a microneedle or an array of microneedles and the therapeutic agent (e.g., protein or RNA-protein granule) is administered subsequently, for example by a needle-free injection technique or by topical administration (e.g. in a liquid or semi-solid formulation, such as an ointment, a cream, a gel or a lotion).
  • the therapeutic agent e.g., protein or RNA-protein granule
  • topical administration e.g. in a liquid or semi-solid formulation, such as an ointment, a cream, a gel or a lotion.
  • a solid microneedle or the solid microneedles in an array as used herein can optionally be polymer based such that the microneedle dissolves over time once applied to a human subject, as in via a patch.
  • the microneedle is a hydrogel-forming microneedle.
  • the protein or RNA-protein granule is administered transdermally to a subject by using a hydrogel-forming microneedle or an array of hydrogel forming microneedles.
  • Hydrogel-forming microneedles are composed of polymers that swell when inserted into the skin, thereby forming channels, through which the therapeutic agent (e.g., protein or RNA-protein granule) can be delivered.
  • microneedle arrays comprising a protein or synthetic RNA-protein granule.
  • Microneedle arrays comprise a plurality of microneedles, e.g., assembled on one side of a supporting base or patch.
  • Various microfabrication methodologies can be used to manufacture microneedle arrays from materials including silicon; metals such as stainless steel, palladium, nickel and titanium carbohydrates including galactose, maltose and polysaccharide, glass, ceramics and various polymers (e.g., PGLA and/or PEG).
  • the protein or RNA-Protein granules described herein are administered to a subject via a microneedle patch that comprises an array of microneedles.
  • microneedle patches include a scaffold with one or more microneedles extending from the scaffold.
  • the microneedle patch includes an array of microneedles, e.g., from 5 to 10,000 microneedles.
  • the microneedle patch can be a variety of sizes, shapes, surface areas, and/or dimensions suitable for administration to a patient (e.g., a human subject).
  • the patch has a surface area of 1 cm 2 to 20 cm 2 , 1 cm 2 to 30 cm 2 , 1 cm 2 to 40 cm 2 , 1 cm 2 to 50 cm 2 , 1 cm 2 to 60 cm 2 , 1 cm 2 to 70 cm 2 , 1 cm 2 to 80 cm 2 , 1 cm 2 to 90 cm 2 , 1 cm 2 to 100 cm 2 , 1 cm 2 to 120 cm 2 , 1 cm 2 to 140 cm 2 , 1 cm 2 to 150 cm 2 , 1 cm 2 to 160 cm 2 , 1 cm 2 to 180 cm 2 , or 1 cm 2 to 200 cm 2 , 2 cm 2 to 14 cm 2 , 20 cm 2 to 50 cm 2 , 50 cm 2 to 100 cm 2 , 100 cm 2 to 150 cm 2 , or 150 cm 2 to 200 cm 2 .
  • the patch has a surface area of 2 cm 2 to 14 cm 2 .
  • the one or more microneedles have a height from about 100 ⁇ m to about 2000 ⁇ m, from about 100 ⁇ m to about 1500 ⁇ m, from about 100 ⁇ m to about 1000 ⁇ m, or from about 500 ⁇ m to about 1000 ⁇ m.
  • the one or more microneedles may be arranged on a base substrate in any suitable density. For example, a plurality of microneedles may be arranged in even or staggered rows in an array.
  • the microneedle patch can be designed to deliver the therapeutic agent (e.g., protein or RNA-Protein granule) at a dissolution rate necessary to achieve a desired dose in a subject.
  • the patch administers 25% of the dose of the therapeutic agent upon initial application with gradual dosing to day 25, and finishing with a 25% dose by day 30.
  • the patch administers 50% of the dose of the therapeutic agent on initial application with the bolus dose of the remaining material at day 30.
  • the patch administers a gradual initial dosing of the therapeutic agent from day 1 to day 25.
  • the patch administers a bolus dose of the therapeutic agent from day 25.
  • a plurality of microneedles may include from 5 to 10,000 microneedles, such as from 50 to 1000 microneedles or from 50 to 200 microneedles.
  • the number of microneedles on the surface of the scaffold may be selected based on a desired application.
  • the microneedle patch may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 14, at least 16, at least 18, at least 20, at least 22, at least 24, at least 26, at least 28, at least 30, at least 32, at least 34, at least 36, at least 38, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 2000, at least 3000, at least 4000, at least 5000, at least 6000, at least 7000, at least 8000, etc. microneedles.
  • the number of microneedles may be in a range including and between any two of the following: 1 microneedle, 2 microneedles, 3 microneedles, 4 microneedles, 5 microneedles, 6 microneedles, 7 microneedles, 8 microneedles, 9 microneedles, 10 microneedles, 11 microneedles, 12 microneedles, 13 microneedles, 14 microneedles, 15 microneedles, 16 microneedles, 17 microneedles, 18 microneedles, 19 microneedles, 20 microneedles, 21 microneedles, 22 microneedles, 23 microneedles, 24 microneedles, 25 microneedles, 26 microneedles, 27 microneedles, 28 microneedles, 29 microneedles, 30 microneedles, 31 microneedles, 32 microneedles, 34 microneedles, 35 microneedles, 36 microneedles, 37 microneedles, 38 microneedles, 39 microneedles,
  • the microneedles may each have a maximum length ranging from about 20 ⁇ m to about 1000 ⁇ m, from about 50 ⁇ m to about 1000 ⁇ m, from about 100 ⁇ m to about 1000 ⁇ m, from about 20 ⁇ m to about 500 ⁇ m, or from about 20 ⁇ m to about 250 ⁇ m. In some embodiments, the microneedles may each have a maximum width, ranging from about 10 ⁇ m to about 500 ⁇ m.
  • the microneedles are configured to pierce the skin for the percutaneous administration of an agent.
  • the microneedles are configured to piece the skin at a depth of about 50 ⁇ m to 1000 ⁇ m.
  • the skin comprises the following layers: stratum comeum at a depth greater than 0 ⁇ m to about 20 ⁇ m; epidermis at a depth from about 20 ⁇ m to about 100 ⁇ m; dermis at a depth from about 100 ⁇ m to about 1000 ⁇ m , and subcutis (hypodermis) at a depth greater than about 1000 ⁇ m.
  • the scaffold of the microneedle patch contacts (and temporarily and removably adheres to) the outermost layer of the skin (e.g., the stratum corneum), while the microneedles pierce the skin such that the tips of the microneedles are positioned within (e.g., and do not extend deeper than) the dermis layer of the skin.
  • the outermost layer of the skin e.g., the stratum corneum
  • the microneedles comprise an agent disposed within and/or coated on at least a portion of a composite material.
  • the composite material of each of the microneedles is configured to dissolve after a predetermined period of time after insertion into mammalian skin, and thereby deliver the agent thereto.
  • the composite material is biocompatible and/or biodegradable.
  • the composite material comprises polymer components that are approved by the Federal Drug Administration (FDA) and/or are GRAS (generally recognized as safe) polymers.
  • the composite material comprises polyethylene glycol (PEG), Polylactic-co-glycolic acid (PLGA), polyvinylpyrrolidone (PVP), or one or more additional copolymers
  • compositions disclosed herein can be used in screening methods and assays to identify new therapeutics, e.g., viral inhibitors.
  • a method of selecting an antiviral therapeutic comprising: a. providing a synthetic microcarrier of the invention; b. contacting the synthetic microcarrier with a target non- viral protein or a fragment thereof, in the presence of the antiviral therapeutic; and c. measuring binding of the non- viral protein or a fragment thereof to the microcarrier, wherein decreased binding of the non-viral protein or a fragment thereof to the synthetic microcarrier in the presence of the antiviral therapeutic indicates the antiviral therapeutic is effective; thereby selecting an effective antiviral therapeutic.
  • a method of testing binding of an agent to a viral protein or fragment thereof comprising: a. providing a synthetic microcarrier of the invention; b. contacting the synthetic microcarrier with the agent; and c. detecting binding of the synthetic microcarrier to the agent; thereby testing binding of an agent to a viral protein of a fragment thereof.
  • a method of testing binding of a fragment of a receptor to a target comprising: a. providing a fusion protein of the invention; b. contacting the fusion protein with the target; c. detecting binding of the fusion protein to the target; thereby testing binding of a fragment of a receptor to a target.
  • the method is a method of selecting an effective antiviral therapeutic. In some embodiments, the method further comprises selecting an effective antiviral therapeutic. In some embodiments, the antiviral therapeutic is designed to inhibit binding of the viral protein to a target non- viral protein. In some embodiments, the antiviral therapeutic inhibits binding of the viral protein to a target non-viral protein. In some embodiments, a target non-viral protein is the viral protein’s target. In some embodiments, the viral protein is a peplomer or a receptor binding fragment thereof and the target protein is the protein used for viral entry. In some embodiments, the target protein is the receptor used by the virus to enter cells. In some embodiments, the non-viral protein is a receptor. In some embodiments, the synthetic microcarrier comprises the viral protein or fragment thereof. In some embodiments, the fragment is a fragment capable of binding the target non- viral protein.
  • the contacting is in the presence of the antiviral therapeutic and in the absence of the antiviral therapeutic.
  • the method further comprises contacting the synthetic microcarrier with the non-viral protein in the absence of the antiviral therapeutic.
  • the measuring is also in the absence of the antiviral therapeutic.
  • decreased is as compared to a predetermined value.
  • the predetermined value is optimal binding.
  • the predetermined value is uninhibited binding.
  • the predetermined value is binding in the absence of the antiviral therapeutic.
  • a decrease in binding in the presence of the antiviral therapeutic as compared to binding the absence of the antiviral therapeutic indicates the antiviral therapeutic is effective.
  • the non- viral protein is a fusion protein of the invention.
  • non-viral protein or fragment thereof comprises a detectable moiety.
  • the agent comprises a detectable moiety.
  • non- viral protein or fragment thereof is conjugated to a detectable moiety.
  • the agent is conjugated a detectable moiety.
  • the measuring comprises detection of the detectable moiety.
  • the measuring comprises measuring the output of the detectable moiety.
  • the output is fluorescence.
  • the measuring comprises detecting the detectable moiety at the microcarrier.
  • the measuring comprises detecting the detectable moiety from the microcarrier.
  • the agent is an antibody or antigen binding fragment thereof.
  • the antibody or antigen binding fragment thereof is to the viral protein or a fragment thereof.
  • the agent is a small molecule. In some embodiments, the small molecule is designed to bind to the viral protein or a fragment thereof. In some embodiments, the agent is a synthetic peptide. In some embodiments, the synthetic peptide is designed to bind to the viral protein or a fragment thereof. In some embodiments, the agent is a synthetic RNA-protein granule. In some embodiments, the granule comprises an agent. In some embodiments, the protein in the granule is an agent. In some embodiments, the granule comprises a protein that binds to the viral protein or a fragment thereof. In some embodiments, the granule comprises an antibody, small molecule or synthetic peptide.
  • the granule comprises a natural peptide.
  • the natural peptide binds to the viral protein or a fragment thereof.
  • the granule comprises an antibody, small molecule, synthetic peptide or natural peptide.
  • the granule is a granule of the invention.
  • the detecting comprises isolating the synthetic microcarrier. In some embodiments, the detecting comprises isolating the target and detecting the fusion protein. In some embodiments, the detecting comprises isolating the fusion protein and detecting the target. In some embodiments, the detecting is detecting the non-viral protein or fragment thereof on the isolated synthetic microcarrier. In some embodiments, the detecting is detecting the non-viral protein or fragment thereof with the isolated synthetic microcarrier. In some embodiments, the detecting is detecting the agent on the isolated synthetic microcarrier. In some embodiments, the detecting is detecting the agent with the isolated synthetic microcarrier. In some embodiments, the detecting comprises microscopy analysis.
  • the microscopy analysis comprises analyzing colocalization. In some embodiments, colocalization is colocalization of the fusion protein and the target. In some embodiments, the microscopy analysis comprises analyzing colocalization of the synthetic microcarrier and the non-viral protein. In some embodiments, the microscopy analysis comprises measuring colocalization of the synthetic microcarrier and the non-viral protein. In some embodiments, the microscopy analysis comprises analyzing colocalization of the synthetic microcarrier and the agent. In some embodiments, the microscopy analysis comprises measuring colocalization of the synthetic microcarrier and the agent.
  • the microcarrier comprises a first detectable moiety and the non-viral protein comprises a second detectable moiety and colocalization is colocalization of the detectable moieties.
  • the microcarrier comprises a first detectable moiety and the agent comprises a second detectable moiety and colocalization is colocalization of the detectable moieties.
  • the fusion protein comprises a first detectable moiety and the target comprises a second detectable moiety and colocalization is colocalization of the detectable moieties.
  • the detectable moieties are a first fluorophore and a second fluorophore.
  • the detecting comprises flow cytometric analysis.
  • the flow cytometric analysis is of the synthetic microcarriers for fluorescence from the fluorophore.
  • the detecting is detecting from the synthetic microcarrier fluorescence produced by the non-viral protein.
  • the detecting is detecting from the synthetic microcarrier fluorescence produced by the agent.
  • the flow cytometric analysis is of the fusion protein for fluorescence from the fluorophore.
  • the flow cytometric analysis is of the target for fluorescence from the fluorophore. Methods of microscopy and flow cytometry are well known in the art and disclosed herein.
  • the target is immobilized on a support.
  • the target is conjugated to a support.
  • the support is isolated.
  • the support is detected.
  • flow cytometry is on the support.
  • colocalization is colocalization at the support.
  • the contacting is in conditions suitable for binding of the viral protein or a fragment thereof to the non-viral protein of a fragment thereof. In some embodiments, the contacting is in conditions suitable for binding of the non-viral protein of a fragment thereof to the microcarrier. In some embodiments, the contacting is in conditions suitable for binding of the viral protein or a fragment thereof to the agent. In some embodiments, the contacting is in conditions suitable for binding of the agent to the microcarrier. Conditions suitable for binding including temperature, salt content and the like can be easily determined by one skilled in the art.
  • the contacting is in the presence of a blocking agent.
  • a blocking agent inhibits non-specific binding to the synthetic microcarrier.
  • inhibiting is blocking.
  • Blocking agents are well known in the art and commercially available and any such blocking agent may be used.
  • the blocking agent is bovine serum albumen (BSA).
  • the concentration of BSA is between 1-50, 1-45, 1-40, 1-35, 1-30, 1-25, 1-20, 1-15, 1-10, 1-5, 2-50, 2-45, 2- 40, 2-35, 2-30, 2-25, 2-20, 2-15, 2-10, 2-5, 3-50, 3-45, 3-40, 3-35, 3-30, 3-25, 3-20, 3-15, 3- 10, 3-5, 4-50, 4-45, 4-40, 4-35, 4-30, 4-25, 4-20, 4-15, 4-10, 4-5, 5-50, 5-45, 5-40, 5-35, 5- 30, 5-25, 5-20, 5-15, and 5-10 ug per microlite of microcarrier. Each possibility represents a separate embodiment of the invention.
  • the concentration of BSA is between 5-10 ug per microlite of microcarrier.
  • the contacting is for between 10-240, 10-180, 10-120, 10- 90, 10-60, 10-30, 20-240, 20-180, 20-120, 20-90, 20- 60, 20-30, 30-240, 30-180, 30-120, 30- 90 and 30-60 minutes. Each possibility represents a separate embodiment of the invention.
  • the contacting is for between 30 and 60 minutes.
  • the contacting is at room temp.
  • the contacting is at about 4 degrees Celsius.
  • the contacting is at about 37 degrees Celsius.
  • the decrease is a significant decrease. In some embodiments, significant is statistically significant. In some embodiments, the decrease is to below a predetermined threshold. In some embodiments, the threshold is a threshold of binding. In some embodiments, the threshold is the binding in the presence of a known effective antiviral therapeutic. In some embodiments, the decrease is a decrease of at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 92, 95, 97, 99 or 100%. Each possibility represents a separate embodiment of the invention. In some embodiments, the decrease is a decrease of at least 10%. In some embodiments, the decrease is a decrease of at least 50%.
  • a coat protein (CP)-spike fusion protein for example, a library of different SARS2 spike variants. Preparation of a library containing variants of the spike protein - which are then fused to a phase coat protein and used in an RNA-protein granule as described herein, provides a composition and method for a panvariant vaccine.
  • the variant library can be produced using an ML-based tool that will have as training data all known spike variants of a given virus to date.
  • RNA protein granules To produce such prophylactic RNA protein granules, the tdCP-spike library is expressed and purified. Granules are then constructed whereby slncRNA are going to be labelled with a fluorescent-uracil to ensure that fluorescent co-localization can be detected. Beads can then be sued to test whether spike granules form clusters with the beads - meaning that they are functional.
  • non-fluorescent ACE2 could be conjugated to beads and mixed with an FP-labelled spike or spike library. A screen could then be performed to identify co localization and inhibition of co-localization.
  • a further aspect of therapeutic screening using the non-fluorescent soluble receptor includes constructing a slncRNA labelled with a fluorescent uracil containing three or less hairpin binding sites (slncRNA ⁇ 3x). slncRNAs with three hairpin or less do not generally form granules (described in more detail in the Examples below).
  • non- fluorescent ACE2P e.g., tdPP7-ACE2(1...740)
  • binds the slncRNA ⁇ 3X This is then mixed with RBD-beads and co-localization is reviewed in order to determine functionality. If co-localization is observed, the assay is successful for can screening inhibitors as with the fluorescent version of ACE2P.
  • RBD mammalian expression and purification A plasmid encoding SARS-Cov-2 RBD was transformed into E. coli TOP10 cells (Invitrogen) and miniprepped (ZymoPure plasmid miniprep II, Zymo). 293F cells were cultured in 30 ml Freestyle 293 [supplemented with penicillin-streptomycin solution (Biological Industries) at 0.5% v/v] expression medium (Thermo Fisher), in 125 ml flat-bottom flasks (TriForest), at 37 °C with 8% CO2 and 135 r ⁇ m shaking. 24h before transfection, cells were passed at 0.6-0.7e6 cells/mL and grown overnight.
  • cells were diluted to le6/ml cell concentration and were then transfected as follows: 37.5 ⁇ g plasmid DNA and 120 pi. of 0.5 mg/ml branched polyethylenimine (PEI, MW -25,000, Sigma Aldrich) were separately brought to 600 m ⁇ in Opti-MEM (Gibco), and incubated for 5 min. PEI solution was added to DNA solution and incubated at room temperature for 15 min. 1200 m ⁇ PEI+DNA solution was added to the 30 ml culture.
  • PEI 0.5 mg/ml branched polyethylenimine
  • the buffer of the eluted RBD was changed to phosphate buffered saline (PBS: Dulbecco's phosphate buffered saline -calcium -magnesium, Biological Industries) by rinsing multiple times with lx PBS on a 3 kDa MWCO spin column (Amicon Ultra 0.5 mL, Merck Millipore). RBD was stored at -20 °C. Lengths of RBD and all other proteins in this work were verified by SDS polyacrylamide gel (SDS-PAGE) followed by Coomassie staining.
  • PBS Dulbecco's phosphate buffered saline -calcium -magnesium, Biological Industries
  • hACE2-mCherry-tdPP7 (hACE2F) mammalian expression and purification:
  • the plasmid encoding hACE2-tdPP7 with a C-terminal his tag was ordered from Twist Bioscience (using different coding sequences for the two copies of PP7 coat protein) and modified in the lab to add mCherry.
  • the transfection, growth, expression, and purification were similar to RBD expression.
  • Typical hACE2F yield was ⁇ 1 mg from 90-120 mLof 293F culture.
  • the culture, supernatant, and Ni-coated beads were visibly pale pink during expression and purification stages.
  • the 2-3 mL hACE2F sample was dialyzed twice against 800 mL of lx PBS + 10 ⁇ M ZnC1 (Pur-A-Lyzer Maxi 3500 dialysis unit, Sigma Aldrich), further concentrated on a 3 kDa MWCO spin column (Amicon Ultra 0.5 mL, Merck Millipore), and stored at -20 °C.
  • mCherry bacterial expression and purification A bacterial plasmid encoding his- tagged mCherry under the rhlR promoter (containing the las box, inducible by C4-HSL), ampicillin resistance, and RhlR was transformed into E. coli TOP10 cells (Invitrogen). Cells containing the plasmid were grown in 10 ml Luria-Bertani medium (LB: 10 g NaCl, 10 g tryptone, and 5 g yeast extract in 1 L deionized water, autoclaved) containing 100 ⁇ g/ml ampicillin (Amp) in a 50 ml falcon overnight, at 37 °C and 250 rpm.
  • LB 10 g NaCl
  • 10 g tryptone 10 g tryptone
  • yeast extract in 1 L deionized water
  • the culture was diluted into 500 ml terrific broth (TB: 24 g yeast extract, 20 g tryptone, 4 ml glycerol in 1 L of water, autoclaved, and supplemented with 17 mM KH2PO4 and 72 mM K2HPO4) containing 100 ⁇ g/ml Amp and 97 pM C4-HSL in a 2-liter flask and grown for another day at 37 °C and 250 rpm. Culture was visibly pink the next morning.
  • resuspension buffer 50 mM Tris, 100 mM NaCl, 0.02% sodium azide in deionized water, pH 7.0.
  • the resuspended cells were lysed by passing the culture four times through a high-pressure homogenizer (Emulsiflex, Avestin Inc, Canada) at an average working pressure of 10-15 kpsi and maintained at 4 °C using a circulating bath (GMBH, Germany). Collected lysate was centrifuged at 13 krpm for 30 min.
  • Typical mCherry yield was 10 mg from 500 mL of TB culture.
  • mCherry buffer was changed by rinsing multiple times with lx PBS on a 3 kDa MWCO spin column, and mCherry was stored at -20 °C.
  • tdPP7-mCherry bacterial expression and purification See details for mCherry expression and extraction, with mCherry replaced by mCherry-tdPP7.
  • Sb#68 bacterial expression and purification His-tagged Sb#68 (ordered as a gBlock from Integrated DNA Technologies, IDT) was expressed from a pET9D bacterial plasmid under a T7 promoter, in E. coli KRX cells (Promega). Growth and expression were similar to mCherry, only with 25 ⁇ g/ml kanamycin instead of Amp, and with 0.1% w/v rhamnose instead of C4-HSL for induction. Extraction and buffer change to lxPBS were the same as described earlier for mCherry. Sb#68 yield was ⁇ 5 mg from 500 mL of TB culture.
  • MES buffer 0.5 M 2-(N-Morpholino) ethanesulfonic acid (Sigma Aldrich) in deionized water, at pH5; diluted to 50 mM in deionized water].
  • the sample was vortexed until particle aggregation was not visible and the mixture looked “milky”.
  • the sample was centrifuged again for 15 min at 3000xg and the supernatant was replaced with 50 pi.
  • EDC N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride
  • the sample was centrifuged for 15 min at 3000xg and the supernatant was replaced with 100 ⁇ l of 1x PBS + 10 ⁇ M ZnC1 2 , 3 times.
  • the synthesized v-particle stock was stored at 4 °C.
  • Final fluorescent particle concentration in the v-particle stock is approximately 1% w/v.
  • the number of particles in 1 mL is approximately 35c10 L 9 for 0.8 ⁇ m particles at 1% w/v (https://www.spherotech.com/particle.html).
  • the maximum covalent attachment ratio of RBD to the particles is 50 peq/g (equal to the manufacturer's claim of 50 peq/g carboxyl groups). This yields a maximum ratio of approximately 3c10 L 5 RBD per particle, based solely on the number of available functional groups. The actual ratio is likely lower due to partial binding, protein size, and steric effects.
  • slncRNA-PP7bsxl4 synthesis DNA encoding a T7 promoter followed by 14 binding sites of bacteriophage PP7 coat protein with EcoRI restriction sites on both ends was ordered as a gBlock (IDT), cloned into a pCMV cloning vector in E. coli TOP10 (Lucigen) using the EcoRI sites, miniprepped, restricted with EcoRI (New England Biolabs, NEB), and column-cleaned.
  • IDT gBlock
  • slncRNA-PP7bsxl4 was transcribed in vitro from the resulting DNA (HiScribe T7 High Yield RNA Synthesis Kit, NEB), purified (Monarch RNA Cleanup Kit, NEB), and stored at -80 °C for later use.
  • Example 1 v-particles are specific and highly sensitive to human ACE2
  • a novel particle-based fluorescence assay for rapid screening of candidate inhibitors of RBD-hACE2 interaction (SARS-CoV-2 receptor binding domain (RBD) (see Fig. 1A).
  • SARS-CoV-2 receptor binding domain RBD
  • This assay utilizes a fluorescent version of hACE2 (containing mCherry, SEQ ID NO: 9), which eliminates the use of antibodies and any related labeling and rinsing steps.
  • Fluorescent particles covalently coated with RBD are used, which are termed v-particles, as the surface on which binding occurs.
  • the v-particles provide a number of benefits: first, during v-particle preparation, unattached RBD can be removed from the v-particle stock via centrifugation, so that all RBD-binding events occur at the v-particle surface. Second, v-particles can be prepared with any choice of viral proteins (e.g., various RBD mutants) or be changed to display any desired component without necessitating a particular chemical modification (Fig. IB).
  • v-particles are large enough to be easily detectable using either flow cytometry or standard fluorescence microscopy and enable clear distinction of bound hACE2 from unbound hACE2 when assayed via flow cytometer or microscope without the need for cleanup via centrifugation or buffer exchange.
  • the RBD for the v-particles was expressed from a plasmid encoding his-tagged RBD (SEQ ID NO: 19).
  • RBD was extracted from Freestyle 293F cells (Thermo Fisher) following the manufacturer's protocol (see Materials and Methods). It was noted that the RBD contains post-translational modifications that are not enzymatically supported in bacterial cells.
  • SPHERO carboxyl fluorescent yellow particles with 0.7-0.9 ⁇ m diameter were purchased (Spherotech Inc., specified batch diameter was 0.92 ⁇ m).
  • the RBD protein was attached to the particles by two-step carbodiimide crosslinker chemistry (see Fig.
  • a His-tagged, fluorescently labeled, version of hACE2 we expressed and secreted from HEK 293F cells, similar to the RBD expression described earlier (see Materials and Methods). Initially, a plasmid encoding a fusion protein of hACE2 to mCherry was used however very low expression was observed and isolation via the His-tag produced no detectable hACE2 protein (Fig. 5, lane 9). A fusion protein with hACE2 and a tandem dimer (td) of PP7 coat protein proved to be highly expressed and highly isolatable via the His-tag (Fig. 5, lane 3).
  • hACE2-mCherry-tdPP7 SEQ ID NO: 9
  • the 2-3 mL hACE2F sample was dialyzed twice against 800 mL of lx PBS + 10 ⁇ M ZnC1 (Pur-A-Lyzer Maxi 3500 dialysis unit, Sigma Aldrich), further concentrated on a 3 kDa MWCO spin column (Amicon Ultra 0.5 mL, Merck Millipore), and stored at -20 °C.
  • BSA Bovine serum albumin
  • v-particle stock was mixed with 1 ⁇ g of mCherry, and 0, 2, 5, 7, 10, or 20 ⁇ g BSA, and the volume was adjusted to 5 m ⁇ with lx PBS.
  • v-particles were replaced with amine polystyrene fluorescent yellow particles (NH 2 -beads, Spherotech, Inc). The samples were incubated at 37 °C with 145 r ⁇ m horizontal shaking for 45 min, covered in aluminum foil. All sample volumes were adjusted to 100 pi with lx PBS and measured via flow cytometry (MACSquant VYB, Miltenyi Biotec).
  • the flow cytometer was calibrated before analysis, and 2 pi of 1% w/v NEb- beads or carboxyl polystyrene fluorescent yellow particles (Spherotech, Inc.) in 100 m ⁇ lxPBS were run as a negative control. Based on the results of the BSA assay (Fig. 2A) a working amount of 5 -10 ⁇ g BSA per 1 m ⁇ of v-particle stock in the binding reactions was established.
  • Fig. 2B the optimal time for binding reactions was determined (Fig. 2B).
  • 1 m ⁇ of pre-sonicated v-particle stock, 10 ⁇ g of BSA, and 2 ⁇ g of hACE2F were added, and the volume was adjusted to 5.5 m ⁇ with lx PBS + 10 ⁇ M ZnC 1 2 ⁇
  • the samples were incubated at 37 °C with 145 rpm horizontal shaking for different amounts of time: 15, 30, 45, 75, 135, and 255 min, and 48hr, covered in aluminum foil. All sample volumes were adjusted to 100 m ⁇ with lx PBS + 10 ⁇ M ZnC 1 2 for flow cytometry . Based on the results (Fig. 2B), 45 min was determined to be sufficient for binding reactions.
  • v-particle binding to either hACE2F or mCherry was measured as follows. In a Lo-Bind microcentrifuge tube, 2.5 m ⁇ of pre-sonicated v- particle stock, 15 ⁇ g of BSA and either 1, 3, or 5 ⁇ g hACE2F, or 0.75 or 7.5 ⁇ g mCherry were combined. Sample volumes were adjusted to 14 pi.
  • v-particles incubated with comparable amounts of hACE2F a fluorescent population of v-particles emerges corresponding to a 2-3 orders of magnitude shift in fluorescence from the non-fluorescent controls, indicating specific binding of hACE2F to the RBD displayed on the v-particles.
  • the dose response observed here is a digital-like increase in the fluorescent bead-fraction rather than an analog shift of the bead population from no- fluorescence to full-fluorescence values.
  • Example 2 Inhibitor screen of RBD-hACE2 interaction
  • hACE2F was added to all the samples, for maximum sensitivity to inhibitor activity.
  • v-particles were replaced with NH 2 -beads.
  • the samples were incubated at 37 °C with 145 rpm horizontal shaking for 45 min covered in aluminum foil.
  • the volume was adjusted to 100 m ⁇ with lx PBS + 10 ⁇ M ZnC1 2 prior to flow cytometry.
  • the flow cytometry results for the different Sb#68 concentrations are plotted in Figure 3A.
  • the high-fluorescence population indicating RBD-hACE2F binding were observed (Fig. 3A, top).
  • RNA-protein (SRNP) granules were utilized to assess the efficacy of synthetic RNA-protein (SRNP) granules in binding, and thereby trapping, SARS-CoV-2 virions.
  • SRNP RNA-protein
  • the v- particles provide a safe and microscopically visible alternative to actual virions.
  • RNAP granules can be produced in vitro and have been shown to bind cellular components. It was recently shown that SRNP granules form specifically in vitro via self-assembly by mixing purified bacterial phage coat proteins (CPs) with synthetic long non-coding RNA (slncRNA) molecules that encode multiple binding sites for the CPs.
  • CPs purified bacterial phage coat proteins
  • slncRNA synthetic long non-coding RNA
  • the protein component in the granule formulation was either tdPP7-mCherry, or hACE2F.
  • the slncRNA component (slncRNA-PP7bsxl4, see Materials and Methods for synthesis details) harbors 14 PP7 binding sites, to which the tdPP7 domain present in both hACE2F and tdPP7-mCherry can bind.
  • the RNA thus increases the local concentration of hACE2F, which may facilitate virion entrapment and thus potentially function as an anti-SARS-CoV-2 decoy particle.
  • SRNP experiments were performed in granule buffer (GB: 750 mM NaCl, 1 mM MgC12, 10% PEG 4000, in water). Reactions containing 8 pi.
  • GB 1 ⁇ g tdPP7-mCherry or 1.5 ⁇ g hACE2F (in 1 pi), 0 or 1 ⁇ g slncRNA-PP7bsxl4 (in 1 ⁇ l), and 0.5 m ⁇ Ribolock RNase Inhibitor (Thermo Fisher Scientific) were incubated at room temperature for 1 hr. After 1 hr, 1 pi. from each reaction was deposited on a glass slide, together with 1 pi. of pre-sonicated 1% w/v v-particle stock diluted 1:5 in water. A 1 pi. control sample of undiluted v-particle stock was also deposited.
  • hACE2F-SRNP-granules appear to be bound to the v-particles (Fig. 4, bottom-right), as compared with the non-hACE2F-SRNP- granules which appear to be spatially separated from the v-particles (Fig. 4, bottom- left). Consequently, the SRNP-hACE2F granules provide a potential decoy or anti-SARS-CoV-2 therapeutic.
  • an assay that enables rapid, cell-free screening of candidate inhibitors of protein-protein interaction.
  • the assay materials are commercially available or relatively easy to prepare, and do not include antibody components.
  • the main difficulty in assay preparation is the production of the protein components. Depending on available lab resources, researchers may choose to outsource this step. And a novel use of bacteriophage coat proteins is herein exemplified that enables enhanced production of some of these components.
  • the utility of the assay is demonstrated, such as for quantifying inhibition of RBD-hACE2 interaction by the reported inhibitor Sb#68, as well as with a potential anti- SARS-CoV-2 RNP-granule decoy particle.
  • v-particles can provide a safe alternative to biohazardous virions for assessing proposed virus entrapment products.
  • This example describes a cell-free assay for rapid screening of candidate inhibitors of protein binding, focusing on inhibition of the interaction between the SARS-CoV-2 Spike receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (hACE2).
  • the assay has two components: fluorescent polystyrene particles covalently coated with RBD, termed virion-particles (v-particles), and fluorescently-labeled hACE2 (hACE2F) that binds the v-particles.
  • v-particle - hACE2F binding When incubated with an inhibitor, v-particle - hACE2F binding is diminished, resulting in a reduction in the fluorescent signal of bound hACE2F relative to the non-inhibitor control, which can be measured via flow cytometry or fluorescence microscopy.
  • RNA-hACE2F granules trap v-particles effectively, providing a basis for potential RNA-hACE2F therapeutics.
  • SARS-CoV-2 virions enters the host cells via interaction between the receptor binding domain of the viral Spike protein (RBD), and hACE2 on the host cell surface 3,4 .
  • RBD receptor binding domain of the viral Spike protein
  • An assay for characterization of RBD-hACE2 binding and the inhibition of this binding could be used to quantify the effect of neutralizing antibodies on the interaction of hACE2 with RBDs of emerging viral strains 5 .
  • it could be used to screen candidate small molecule inhibitors of RBD-hACE2 binding, thereby accelerating the inhibitor identification step of drug discovery 6 .
  • assay results may differ between labs due to differences in cell strain, growth conditions, and inherent variability in biological response.
  • Pseudovirs assays for SARS-CoV-2 inhibitors 11,12 require only Biosafety Fevel 2, but may still suffer from relatively high expense and inherent variability due to the cellular component. These constraints provide motivation for cell-free screening alternatives 13 .
  • a cell-free assay for screening of inhibitors of protein-protein interaction should satisfy the following requirements: detection using standard lab equipment, repeatability, ease of use, flexibility, and low cost. Since protein sizes are well below the optical diffraction limit, some form of bulk measurement is required.
  • RBD-hACE2 inhibitors Commercial Chemical, Cat. 502050
  • Horseradish peroxidase (HRP)-hACE2 is introduced in the presence or absence of an inhibitor candidate. Excess HRP-hACE2 is rinsed, and HRP activity is measured optically at 450 nm via plate reader.
  • the v-particles provide a number of benefits: first, during v-particle preparation, unattached RBD can be removed from the v-particle stock via centrifugation, so that all RBD-binding events occur at the v-particle surface. This could enable production of a ready-to-use product that can be more easily shipped and stored than a coated microplate. Such a ready-to-use product could enable better quality control of the assay and yield more reproducible results 17 . Second, the v-particles provide a versatile platform: v-particles can be prepared with any choice of viral proteins (e.g., various RBD mutants) or be adapted to display any desired component without necessitating a particular chemical modification.
  • v-particles can be prepared with any choice of viral proteins (e.g., various RBD mutants) or be adapted to display any desired component without necessitating a particular chemical modification.
  • v-particles are large enough to be easily detectable using either flow cytometry (Fig. 19A) or standard fluorescence microscopy and enable clear distinction of bound hACE2 from unbound hACE2 when assayed via flow cytometer or microscope without the need for cleanup via centrifugation or buffer exchange.
  • RBD for the v-particles in the presented data was purchased from RayBiotech [Recombinant SARS-CoV-2, SI Subunit Protein (RBD), cat. 230-30162]. Similar results were obtained for RBD expressed in our lab from a plasmid encoding his-tagged RBD that was a gift from the Krammer lab (see sequence in Table 2). Lab-produced RBD 18 was extracted from HEK293F cells (Freestyle 293, Thermo Fisher) following the manufacturer's protocol (for full details, see Supplementary Methods). For v-particle generation, carboxyl fluorescent yellow particles with 0.7-0.9 ⁇ m diameter were purchased (Spherotech Inc., cat. CFP-0852-2, lot no.
  • the RBD protein was attached to the particles by two-step carbodiimide crosslinker chemistry (see Fig. 1A) using N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC, Sigma Aldrich) and N-hydroxysulfosuccinimide sodium salt (Sulfo-NHS, Sigma Aldrich). (See Supplementary Methods for full details.)
  • hACE2F was expressed and secreted from HEK293F (Freestyle 293, Thermo Fisher) cells. We refer to this protein as hACE2F in the following. (See Table 2 for hACE2F sequence, and Supplementary Methods for hACE2F expression and purification.)
  • RNA-protein (SRNP) granules can be produced in vitro 21,22 , and have been shown to bind cellular components 22,23 .
  • SRNP granules form specifically in vitro via self-assembly by mixing purified bacterial phage coat proteins with synthetic long non-coding RNA (slncRNA) molecules that encode multiple binding sites for the coat proteins.
  • the protein component in the granule formulation was either tdPP7- mCherry, or hACE2F (see Supplementary Methods and Table 2 for both proteins).
  • the slncRNA component (slncRNA-PP7bsxl4, see Table 2 for sequence and Supplementary Methods for synthesis details) harbors 14 PP7 binding sites, to which the tdPP7 domain present in both hACE2F and tdPP7-mCherry can bind.
  • RNA thus increases the local concentration of hACE2F, which may facilitate virion entrapment and thus potentially function as an anti-SARS-CoV-2 decoy particle (Fig. 22A).
  • v-particles with slncRNA-PP7bsxl4 and tdPP7-mCherry we prepared the following samples: v-particles with hACE2F, and v-particles with slncRNA-PP7bsxl4 and hACE2F.
  • Fig. 22 In the microscopy images, v-particles appear as green-fluorescent beads (Fig.
  • SRNP-granules appear as large red clumps or as bead-like particles (Fig. 22C), which are located on the cover slip at different positions from the v-particles.
  • Fig. 22C When v-particles are mixed with hACE2F, colocalization of the hACE2F protein to the v-particles is observed, as expected from our previous experiments (Fig. 22D).
  • hACE2F-SRNP-granules appear to be bound to the v-particles (Fig. 22E), as compared with the non-hACE2F-SRNP- granules which appear to be spatially separated from the v-particles (Fig. 22C). Consequently, the SRNP-hACE2F granules provide a potential decoy or anti-SARS-CoV-2 therapeutic, which should be examined in follow-up research.
  • v-particles can provide a cell-free alternative to more expensive and higher-biosafety-level cell-based assays for assessing proposed SARS-CoV-2 entrapment products.
  • V-particles and protein components were added according to the details below.
  • Voltages for the SSC, FSC, FITC (Bl) and mCherry (Y2) channels were 400, 200, 325, and 300 V, respectively. Events were defined using an FSC-height trigger of 60, chosen using a bead-only control. Approximately 10,000 events per sample were collected. Of these, typically over 98% were FITC-positive, using a B 1-area threshold of le3. Negative mCherry values (negative Y2-area below zero, indicative of noise distribution around 0, typically less than 10% of FITC-positive events) were assigned a value of zero.
  • Boxplot measurements shown are the mCherry fluorescence values of the FITC-positive events, with black marker indicating the median, colored bar spanning from the 25th to the 75th percentile, and whiskers extending to extreme data points not considered outliers (using the Matlab boxplot function).
  • the synthesized particle stock was stored at 4 °C, and could be used for approximately 3 weeks.
  • Final fluorescent particle concentration in the particle stock is approximately 1% w/v.
  • One bead particle contains up to 300,000 COOH functional groups, and can therefore theoretically bind a maximum of 300,000 protein molecules.
  • a Lo-Bind microcentrifuge tube we combined 0.5 m ⁇ of pre- sonicated protein-particle stock with 99.5 m ⁇ lx PBS and measured by flow cytometry as described above.
  • tdPP7-mCherry we did not add any hACE2F (Fig. 20A).
  • RBD we added a constant amount of 0.34 ⁇ g hACE2F (Fig. 20B).
  • a Lo- Bind microcentrifuge tube we combined 0.5 m ⁇ of pre-sonicated v-particle stock with 10 ⁇ g of BSA and 0.34 ⁇ g hACE2F. Total volume was adjusted to 5 pi. Samples were incubated, diluted, and measured by flow cytometry as described above.
  • RBD SARS-CoV-2 Spike receptor-binding domain
  • hACE2 human angiotensin converting enzyme 2
  • tdPP7 tandem-dimer form of bacteriophage PP7 coat protein
  • hACE2F fluorescently-labeled hACE2 also containing tdPP7
  • slncRNA-PP7bsxl4 synthetic long noncoding RNA harboring 14 binding sites of bacteriophage PP7 coat- protein.
  • RBD mammalian expression and purification The plasmid encoding RBD was a gift from the Krammer lab. The plasmid was transformed into E. coli TOP10 cells (Invitrogen) and miniprepped (ZymoPure plasmid miniprep II, Zymo). 293F cells were cultured in 30 ml Freestyle 293 [supplemented with penicillin- streptomycin solution (Biological Industries) at 0.5% v/v] expression medium (Thermo Fisher), in 125 ml flat- bottom flasks (TriForest), at 37 °C with 8% CO2 and 135 rpm shaking.
  • Freestyle 293 supplied with penicillin- streptomycin solution (Biological Industries) at 0.5% v/v] expression medium (Thermo Fisher), in 125 ml flat- bottom flasks (TriForest), at 37 °C with 8% CO2 and 135 rpm shaking.
  • hACE2-mCherry-tdPP7 (hACE2F) mammalian expression and purification:
  • hACE2-tdPP7 The plasmid encoding the extracellular domain of ACE2 (amino acids 18 to 740) fused to tdPP7 (hACE2-tdPP7) with C-terminal his tag was ordered from Twist Bioscience (using different coding sequences for the two copies of PP7 coat protein), and modified in the lab to add mCherry (see full sequence in Table 2).
  • the transfection, growth, expression, and purification were similar to RBD expression.
  • Typical hACE2F yield was ⁇ 1 mg from 90- 120 mL of 293F culture. The culture, supernatant, and Ni-coated beads were visibly pale pink during expression and purification stages.
  • hACE2F was stored at 5 °C for short-term use (up to a month) or mixed at 1:1 volume ratio glycerol and stored at -20 °C.
  • tdPP7-mCherry bacterial expression and purification A bacterial plasmid encoding his-tagged tdPP7-mCherry (see Table 2 for sequence) under the rhlR promoter (containing the las box, inducible by N-butyryl-L-Homoserine lactone [C4-HSL], Cayman Chemical), ampicillin resistance, and Rh1R was transformed into E. coli TOP 10 cells (Invitrogen).
  • Cells containing the plasmid were grown in 10 ml Luria-Bertani medium (LB: 10 g NaCl, 10 g tryptone, and 5 g yeast extract in 1 L deionized water, autoclaved) containing 100 ⁇ g/ml ampicillin (Amp) in a 50 ml falcon overnight, at 37 °C and 250 rpm.
  • Luria-Bertani medium LB: 10 g NaCl, 10 g tryptone, and 5 g yeast extract in 1 L deionized water, autoclaved
  • Amicillin ampicillin
  • the culture was diluted into 500 ml terrific broth (TB: 24 g yeast extract, 20 g tryptone, 4 ml glycerol in 1 L of water, autoclaved, and supplemented with 17 mM KH2PO4 and 72 mM K2HPO4) containing 100 ⁇ g/ml Amp and 97 nM C4-HSL in a 2-liter flask, and grown for another day at 37 °C and 250 rpm. Culture was visibly pink the next morning.
  • resuspension buffer 50 mM Tris, 100 mM NaCl, 0.02% sodium azide in deionized water, pH 7.0.
  • the resuspended cells were lysed by passing the culture four times through a high-pressure homogenizer (Emulsiflex, Avestin Inc, Canada) at an average working pressure of 10-15 kpsi and maintained at 4 °C using a circulating bath (GMBH, Germany). Collected lysate was centrifuged at 13 krpm for 30 min.
  • Typical tdPP7-mCherry yield was 10 mg from 500 mL of TB culture.
  • tdPP7-mCherry buffer was changed by rinsing multiple times with lx PBS on a 3 kDa MWCO spin column.
  • tdPP7-mCherry was stored at 5 °C for short-term use (up to a month) or mixed at 1:1 volume ratio glycerol and stored at - 20 °C.
  • Sb#15 and Sb#68 bacterial expression and purification The sequences of Sb#15 and Sb#68 were obtained via correspondence with Justin Walter from the lab of Marcus Seeger. We expressed his-tagged Sb#68 and Sb#15 (see Table 2 for sequences, ordered as gBlocks from Integrated DNA Technologies, IDT) from a pET9D bacterial plasmid under a T7 promoter, in E. coli BL21 cells. Growth and expression were similar to tdPP7-mCherry, only with 25 ⁇ g/ml kanamycin (Kan), and with 1 mM isopropyl- ⁇ -D-thiogalactoside (IPTG) for induction.
  • Kan kanamycin
  • IPTG isopropyl- ⁇ -D-thiogalactoside
  • Extraction and buffer change to lx PBS were the same as described earlier for tdPP7-mCherry. Yield was ⁇ 5 mg from 500 mL of TB culture. Plasmids encoding Sb#15 and Sb#16 were deposited to addgene by the Seeger lab (plasmids 153523 and 153527). Sb#15 and Sb#16 were stored at 5 °C for short-term use (up to a month) or mixed with glycerol at 1:1 volume ratio and stored at -20 °C.
  • GS4 bacterial expression and purification The pSBinit plasmid (see Addgene plasmid 110100 for backbone sequence) encoding his-tagged GS4 (see Table 2 for sequence) under a pBAD promoter was a kind gift of the Seeger lab. Growth and expression in E. coli TOP10 cells were similar to tdPP7-mCherry, only with 12.5 ⁇ g/ml chloramphenicol (Cm), and with lx L-arabinose (Lucigen F95194-1 lOOOx, 10% w/v) for induction. Extraction and buffer change to lx PBS were the same as described earlier for tdPP7-mCherry. Yield was ⁇ 5 mg from 1 L of TB culture. GS4 was stored at 5 °C for short-term use (up to a month) or mixed with glycerol at 1:1 volume ratio and stored at -20 °C.
  • MES buffer 0.5 M 2-(N-Morpholino) ethanesulfonic acid (Sigma Aldrich) in deionized water, at pH5; diluted to 50 mM in deionized water].
  • MES stock 0.5 M 2-(N-Morpholino) ethanesulfonic acid (Sigma Aldrich) in deionized water, at pH5; diluted to 50 mM in deionized water].
  • the sample was vortexed until particle aggregation was not visible and the mixture looked “milky”.
  • the sample was centrifuged again for 15 min at 3000xg and the supernatant was replaced with 50 ⁇ l of 50 mM MES containing 0.1 mg N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC, Sigma Aldrich) and 50 m ⁇ of 50 mM MES containing 1.1 mg N- hydroxysulfosuccinimide sodium salt (Sulfo-NHS, Sigma Aldrich). The sample was vortexed and incubated at room temperature with 145 r ⁇ m horizontal shaking for 30 min protected from light.
  • 50 mM MES containing 0.1 mg N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride
  • Sulfo-NHS sodium salt
  • the sample was then centrifuged for 15 min at 3000xg and the supernatant was replaced with 100 m ⁇ of lx PBS, 2 times.
  • the sample was centrifuged for 15 min at 3000xg and the supernatant was replaced with 100 m ⁇ of lx PBS, 3 times.
  • the synthesized v-particle stock was stored at 4 °C.
  • Final fluorescent particle concentration in the v-particle stock is approximately 1% w/v.
  • the number of particles in 1 mL is approximately 35e9 for 0.8 ⁇ m particles at 1% w/v (see https://www.spherotech.com/particle.html).
  • the maximum covalent attachment ratio of RBD to the particles is 50 peq/g (equal to the manufacturer's claim of 50 peq/g carboxyl groups). This yields a maximum ratio of approximately 3e5 RBD per particle and 1.5e5 RBD per particle for 0.5x RBD v-particle, based solely on the number of available functional groups. The actual ratio is likely lower due to partial binding, protein size, and steric effects.
  • slncRNA- PP7bsxl4 was transcribed in vitro from the resulting DNA in a 30 m ⁇ reaction at 37 °C for 3 hours (HiScribe T7 High Yield RNA Synthesis Kit, NEB). The reaction volume of the transcription product was diluted to 90 m ⁇ using UltraPure water (Bio-Lab Ltd.), 10 m ⁇ of DNAse I buffer and 2 ⁇ l of DNAse I (NEB) were added, and the resulting mix was incubated at 37 °C for 15 min. Finally, slncRNA-PP7bsxl4 was purified (Monarch RNA Cleanup Kit 500 ⁇ g, NEB), and stored for later use at -80 °C. Typical concentrations were 100-1000 ng/pl, with 100 m ⁇ final volume.
  • Liquid-solid transition also known as gelation, is a specific form of phase separation in which the interacting molecules cross-link to form a highly interconnected compartment with solid - like dynamical properties.
  • This example describes the use of RNA hairpin coat- protein (CP) binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition.
  • CP RNA hairpin coat- protein
  • This example shows both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta.
  • the example further demonstrates that upon introduction of the coat-proteins (CPs), less- condensed gel-like granules form with the RNA creating an outer shell with the proteins mostly present inside the granule.
  • phase separation the process by which a homogeneous solution separates into multiple distinct phases, has been connected to a wide range of natural cellular processes in virtually all forms of life 1-5 .
  • phase separation results in the formation of membrane- less compartments containing a high-concentration mix of biomolecules (e.g., proteins, RNA, etc.), which are surrounded by a low-concentration solution.
  • biomolecules e.g., proteins, RNA, etc.
  • phase separations are classified by the different material states which can lead to multiple types of transitions (e.g., liquid-solid, gas-liquid, etc.).
  • transitions e.g., liquid-solid, gas-liquid, etc.
  • the forms commonly reported in cellular biology are broadly liquid-liquid and liquid-solid (e.g., gelation), however determining the exact mechanisms for phase separation in a living cellular environment is often challenging 5 .
  • Liquid-liquid phase transitions can be distinguished from liquid-solid by the dynamical properties of the resulting condensates.
  • Liquid-based condensates show rapid internal rearrangement of molecules, fusions between different condensates upon contact, and dependency on the concentration of the molecules in the condensed phase 6,7 .
  • liquid-solid based condensates show none of the above qualities and are mainly dependent on the number of ‘cross-linkers’, which are points of contact between the molecules, rather than on the concentration of the molecules themselves 8-10 .
  • RNA granules both in vivo and in vitro, from highly repetitive RNA sequences associated with repeat expansion diseases. These RNA sequences, comprised of dozens of triplet-repeats of CAG or CUG nucleobases, form intramolecular hairpin structures 12 , which facilitate multivalent intermolecular interactions.
  • the RNA granules presented features associated with liquid- solid phase transition systems: a lack of internal mobility, virtually no fusion events, and dependence on the number of repeats in the RNA sequence (i.e., cross linkers) rather than the concentration of the RNA. These characteristics helped establish the granules as physical solids.
  • RNA sequences are widespread in the RNA world and are not strictly associated with disease phenotypes. Such sequences are commonly used in synthetic systems for biological research. Perhaps the most ubiquitous system is composed of RNA sequences that encode for multiple hairpin motifs that can bind the phage coat proteins (CPs) of PP7 or MS2. Using this system to label the 5’ or 3’ end of a transcript has become commonplace in the last two decades 13-18 , and enables visualization of RNA transcripts when the CPs are co-expressed. This approach, originally introduced by Singer and others 13- 15 , was devised for the purpose of probing the dynamics of transcription and other RNA- related processes, irrespective of cell-type.
  • CPs phage coat proteins
  • Hairpin containing RNA phase separates in vitro into gel-like granules
  • slncRNA synthetic long non-coding RNA binding-site cassettes using a binding site resource 19-21 .
  • slncRNAs six synthetic long non-coding RNA binding-site cassettes using a binding site resource 19-21 .
  • the slncRNAs into two groups.
  • class I slncRNAs three cassettes consisting of three, four, or eight hairpins that encode for PCP binding sites (PCP-3x, PCP-4x, and PCP-8x, respectively) were designed.
  • hairpins were spaced by a randomized sequence that did not encode for a particular structure.
  • slncRNAs For the second group (class II slncRNAs), three cassettes that consisted of three, four, and fourteen PCP binding that were each spaced by hairpin structures that do not bind PCP (PCP- 3x/MCP-3x, PCP-4x/MCP-4x, and PCP-14x/MCP-15x, respectively) were designed.
  • the sequences encoding for the slncRNAs were cloned downstream to a pT7 promoter and transcribed in vitro to generate the corresponding RNA.
  • To visualize the RNA we incorporated fluorescent nucleotides in the transcription reaction such that an estimated 30% of uracil bases were tagged by Atto-488 fluorescent dye.
  • Each slncRNA-type was separately mixed with granule forming buffer (see methods and Fig. 6A) at equal concentration (8.5 nM final concentration) and incubated for 1 hour at room temperature. 2 ⁇ l of the granule reaction were then deposited on a glass slide and imaged using an epi-fluorescent microscope.
  • the images show formation of a multitude of bright localized fluorescent condensates for all slncRNA types except for the PCP-3x case, where no such structures were detected (Fig. 6B).
  • the sequences are described in Table 3, as well as in the Materials and Methods below.
  • the longer slncRNA molecules e.g., PCP-8x and PCP- 14x/MCP-15x
  • PCP-8x and PCP- 14x/MCP-15x also exhibit larger structures, consistent with a gel like solid network, in addition to the smaller condensates or puncta.
  • RNA-based granules co-localize with protein-binding partners
  • PCP-14x/MCP-15x granules seems to be >2-fold brighter as compared with the PCP-8x granules, despite having ⁇ 2-fold the number of hairpins. This stands in contrast to the observation that PCP- 14x/MCP-15x granules appeared to be ⁇ 3 times brighter than PCP-4x/MCP-4x granules, reflecting the difference in the number of binding sites available for binding. Finally, PCP- 3x granules appeared to be half as bright as PCP-14x/MCP-15x granules, providing more evidence that the former are not RNA-dependent entities. It was also observed that when the spacing regions within the slncRNA encode for the MCP hairpins, the formed granules contain a larger protein cargo.
  • FIG. 7E shows a sample image of a PCP-14x/MCP-15x granule containing the tdPCP-mCherry protein.
  • the image shows that slncRNA is found mainly in the periphery of the granule, with filaments protruding into its core, where a high amount of protein is amassed in a network like configuration.
  • the RNA seems to encase the protein cargo in a reduced density structure.
  • the intensity distribution of the puncta declines in a more gradual fashion as the protein concentration is reduced, but overall, a similar disappearance of puncta is observed.
  • phase separation is the exchange of molecules between the dilute phase and the dense phase. This is also true for gels with non-permanent intermolecular interactions, wherein random breaks and rearrangement of the connections which form the inner network allow macromolecules (monomers and small polymers) to diffuse in and out of the gel phase 8-11 , albeit at a slow rate. These exchange events are predicted to occur independently of one another, at a rate which depends on multiple parameters: the probability of cross linking within the gel network (i.e., number of hairpins), the transient concentration of the molecules in the surrounding solution, and the average diffusion rate of the monomers. The movement of molecules (fluorescent CPs, slncRNA, and CP-bound slncRNA complexes) between the different phases should be reflected by changes in granule fluorescence intensity.
  • the events were classified as either increasing bursts (green), decreasing bursts (red), or non-classified segments (blue), which are segments where molecular movement cannot be discerned from the noise (Fig. 8A).
  • a intensity amplitude
  • a time duration
  • Fig. 8B the distributions of amplitudes for all three event types were plotted, obtained from -156 signal traces, each gathered from a different granule composed of PCP- 14x/MCP-15x and tdPCP-mCherry. We observe a bias towards negative burst or shedding events.
  • FIG. 8D shows a sample signal for the PCP- 14x/MCP-15x granules showing concomitant occurrence of bursts in both the red and green channels, supporting our interpretation of this signal.
  • the burst distributions we then computed the ratio between the mean granule fluorescence and the mean burst amplitude, providing a measure for the number of slncRNA molecules within the granule.
  • the results show that with the exception of the PCP-4x based SRNP granules, the ratio in the green channel is 5, suggesting that a typical granule contains five slncRNAs.
  • the ratio computed for the red channel is typically smaller, and for PCP-8x is ⁇ 2.
  • PCP-8x may be permeable to proteins diffusing out of the granules due to reduced cross-linking as a result of a lack of hairpin spacing structures.
  • PCP- 3x/MCP-3x, PCP-4x/MCP-4x, and PCP-14x/MCP-15x the ratio in the red channel is approximately equal to that of the green channel, suggesting that these granules have a better protein storage capacity.
  • the granules composed of class II slncRNA seemed to form more robust and better insulated granules from the perspective of their protein storage capacity.
  • the first slncRNA is of a class II design, PCP-4x/ QCP-5x, consisting of four native PCP binding sites and five native Q ⁇ coat protein (QCP) hairpins used as spacers in an interlaced manner.
  • the second slncRNA is the ubiquitous PCP-24x cassette 25 , which from the perspective of this study can be regarded as a class I design slncRNA.
  • slncRNA component was encoded under the control of a T7 promoter, and the tdPP7-mCherry under the control of an inducible pRhlR promoter (Fig. 9A).
  • a goal was to test whether puncta develop in vivo and whether they are dependent on the existence of hairpins in the RNA.
  • co- transformed plasmids encoding either the negative control RNA or the PCP-4x/QCP-5x slncRNA, together with a plasmid encoding for the tdPCP-mCherry protein, into BL21-DE3 E. coli cells.
  • Examination of cells expressing the slncRNA and protein following overnight induction of all components revealed the formation of bright puncta at the cell poles (Fig.. 9B), which were absent in cells expressing the control RNA which lacks hairpins (Fig. 9C).
  • RNA-protein granules can be designed and assembled using phage coat proteins and RNA molecules that encode multiple CP binding sites, both in suspension and in vivo.
  • fluorescently labelled RNA we show that granule formation is nucleated by RNA-RNA interactions that are proportional to the number of hairpins encoded into the RNA.
  • the binding of the proteins seems to further enhance and assist the granule formation process.
  • fluorescent single molecule signal analysis we reveal entry and exit events of molecules into and out of the granules.
  • slncRNA design a homogeneous design which is comprised of multiple CP hairpin binding site and non-structured spacing regions (class I), and a hybrid design which is comprised of hairpin binding sites and additional hairpins in the spacing regions (class II).
  • class I homogeneous design which is comprised of multiple CP hairpin binding site and non-structured spacing regions
  • II hybrid design which is comprised of hairpin binding sites and additional hairpins in the spacing regions
  • class I granules were characterized by decreased cross-linking in the RNA-only phase and increased permeability of the protein cargo in the SRNP-granule phase.
  • class I granules displayed a faster shedding or dissolution rate, which in turn lead to a smaller protein cargo on average.
  • This two-dimensional phase space of capacity vs. rigidity offers substantial flexibility and tunability when designing SRNP granules for a variety of applications.
  • the capacitor- or storage-like behavior displayed by the SRNP granules implies that in vivo , the granules together with the gene-expression machinery form a biochemical analog of an RC-circuit.
  • energy is stored within the capacitor for release at a later time.
  • Such circuits are often used to protect electrical devices against sudden surges or stoppages of power.
  • the protein and slncRNA flux into the cytosol correspond to the current, which results in the formation of fully “charged" SRNP granules.
  • This genetically encoded slncRNA and protein storage facility which is constantly maintained, effectively increases the protein and slncRNA content of the cell beyond the steady-state levels facilitated by standard transcription, translation, RNA degradation, and proteolysis.
  • This storage capacity is precisely the function that is carried out by capacitors in RC-circuits, allowing electrical devices to function even after "power" is cut-off.
  • the granules can be used not only to increase levels of a protein of choice by nearly an order of magnitude (as shown in Fig. 10) without adversely affecting the cell, but may also provide a mechanism to increase the cell's ability to survive when a harsh or stressful environment is encountered.
  • RNP granules While the former may have important implications to the biotechnology sector, the latter may hint at an important function that natural granules (e.g., paraspeckles, p-bodies, etc.) may have evolved for in vivo. Further studies will be required to explore the biological relevance of RNP granules to the survivability of cells and organisms under various forms of stress.
  • the RNP granules described herein have tremoundous applications for drug delivery.
  • E. coli BL21-DE3 cells which encode the gene for T7 RNAP downstream from an inducible pLac/Ara promoter were used for all reported experiments.
  • E. coli TOP10 Invitrogen, Life Technologies, Cergy-Pontoise was used for cloning procedures.
  • pCR4-24XPP7SL was a gift from Robert Singer (Addgene plasmid # 31864; http://n2t.net/addgene:31864; RRID: Addgene_31864).
  • pBAC-lacZ was a gift from Keith Joung (Addgene plasmid # 13422; http://n2t.net/addgene: 13422; RRID: Addgene_13422).
  • the 5Q ⁇ /4RR7 slncRNA sequence was ordered from GenScript, Inc. (Piscataway, NJ), as part of a puc57 plasmid, flanked by EcoRI and Hind!II restriction sites.
  • pBAC-lacZ backbone plasmid was obtained from Addgene (plasmid #13422). Both insert and vector were digested using EcoRI and HindIII (New England Biolabs [NEB], Ipswich, MA)and ligated to form a circular plasmid. Sequence was verified by sanger sequencing.
  • Fusion-RBP plasmids were constructed as previously reported 21 . Briefly, RBP sequences lacking a stop codon were amplified via PCR off either Addgene or custom- ordered templates. Both RBPs presented (PCP and QCP) were cloned into the RBP plasmid between restriction sites Kpnl and Agel, immediately upstream of an mCherry gene lacking a start codon, under the so-called RhlR promoter containing the rhlAB las box 31 and induced by N-butyryl-L-homoserine lactone (C4-HSL) (Cayman Chemicals, Ann Arbor, Michigan). The backbone contained either an Ampicillin (Amp) or Kanamycin (Kan) resistance gene, depending on experiment.
  • Ampicillin Ampicillin
  • Kanamycin Kanamycin
  • Non-fluorescent RNA was transcribed using the HiScribeTM T7 High Yield RNA Synthesis Kit (NEB, #E2040S). Following in vitro transcription by either kit, the reaction was diluted to 90 pi. and was supplemented with 10 m ⁇ DNAse I buffer and 2 m ⁇ DNAse I enzyme (NEB #M0303S) and incubated for 15 minutes at 37° C to degrade the DNA template. RNA products were purified using Monarch RNA Cleanup Kit (NEB, #T2040S) and stored in -80°.
  • E. coli cells expressing tdPP7-mCherry fusion protein were grown overnight in 10 ml LB with appropriate antibiotics at 37° C with 250 rpm shaking. Following overnight growth cultures were diluted 1/100 into two vials of 500 ml Terrific Broth (TB: 24 g yeast extract, 20 g tryptone, 4 ml glycerol in 1 L of water, autoclaved, and supplemented with 17 mM KH2P04 and 72 mM K2HP04), with appropriate antibiotics and induction (100 m ⁇ C4- HSL) and grown in 37° C and 250 rpm shaking to OD600 > 10.
  • TB 24 g yeast extract, 20 g tryptone, 4 ml glycerol in 1 L of water, autoclaved, and supplemented with 17 mM KH2P04 and 72 mM K2HP04
  • Cells were harvested, resuspended in 30 ml resuspension buffer (50 mM Tris-HCl pH 7.0, 100 mM NaCl and 0.02% NaN3), disrupted by four passages through an EmulsiFlex-C3 homogenizer (Avestin Inc., Ottawa, Canada), and centrifuged (13,300 RPM for 30 min) to obtain a soluble extract. Fusion protein was purified using HisFink Protein purification resin (Promega) according to the manufacturer’s instructions. Buffer was changed to lxPBS using multiple washes on Amicon columns (Biorad).
  • BL21-DE3 cells expressing the two plasmid system were grown overnight in 5 ml Luria Broth (LB), at 37° with appropriate antibiotics (Cm, Amp), and in the presence of two inducers — 1.6 m ⁇ Isopropyl b-D-l-thiogalactopyranoside (IPTG) (final concentration 1 mM), and 2.5 m ⁇ C4-HSL (final concentration 60 ⁇ M) to induce expression of T7 RNA polymerase and the RBP-FP, respectively.
  • LB Luria Broth
  • IPTG Isopropyl b-D-l-thiogalactopyranoside
  • C4-HSL final concentration 60 ⁇ M
  • Overnight culture was diluted 1:50 into 3 ml semi-poor medium consisting of 95% bioassay buffer (BA: for 1 L — 0.5 g Tryptone [Bacto], 0.3 ml glycerol, 5.8 g NaCl, 50 ml 1 M MgS04, 1 ml lOxPBS buffer pH 7.4, 950 ml DDW) and 5% LB with appropriate antibiotics and induced with 1 m ⁇ IPTG (final concentration 1 mM) and 1.5 m ⁇ C4-HSL (final concentration 60 ⁇ M).
  • bioassay buffer BA: for 1 L — 0.5 g Tryptone [Bacto], 0.3 ml glycerol, 5.8 g NaCl, 50 ml 1 M MgS04, 1 ml lOxPBS buffer pH 7.4, 950 ml DDW
  • 5% LB with appropriate antibiotics and induced with 1 m ⁇ IPTG (final concentration 1 mM) and 1.5
  • the tracking data, (x,y,t coordinates of the bright spots centroids), together with the raw microscopy images were fed to a custom built Matlab (The Mathworks, Natick, MA) script designed to normalize the relevant spot data. Normalization was carried out as follows: for each bright spot, a 14-pixel wide sub-frame was extracted from the field of view, with the spot at its center. Each pixel in the sub-frame was classified to one of three categories according to its intensity value. The brightest pixels were classified as ‘spot region’ and would usually appear in a cluster, corresponding to the spot itself. The dimmest pixels were classified as ‘dark background’, corresponding to an empty region in the field of view. Lastly, values in between were classified as ‘cell background’ (Fig.
  • y(t) is the observed spot signal
  • S (t) is the underlying spot signal which we try to extract
  • c(t) is the observed cell background signal
  • c 0 ( t ) is the underlying background signal
  • f(t) is the photobleaching component
  • Identifying burst events [0623] We assume the total fluorescence is comprised of three distinct signal processes: RNP granule fluorescence, background fluorescence and noise. We further assume that background fluorescence is slowly changing, as compared with granule fluorescence which depends on the dynamic and frequent insertion and shedding events occurring in the droplet. Finally, we consider noise to be a symmetric, memory-less process. Based on these assumptions, we define a “signal-burst” event as a change or shift in the level of signal intensity leading to either a higher or lower new sustainable signal intensity level. To identify such shifts in the base-line fluorescence intensity, we use a moving-average filter of 13 points (i.e., 2 minutes) to smooth the data.
  • the effect of such an operation is to bias the fluctuations of the smoothed noisy signal in the immediate vicinity of the bursts towards either a gradual increase or decrease in the signal (Fig. 15A). Random single fluctuations, which do not settle on a new baseline level are not expected to generate a gradual and continuous increase or decrease over multiple time-points in a smoothed signal. Following this, we search for contiguous segments of gradual increase or decrease and record only those whose probability for occurrence is 1 in 1000 or less given a Null hypothesis of randomly fluctuating noise.
  • the threshold is calculated for each signal separately and is usually in the range of 7-13 time points.
  • An analogous threshold is calculated for decrements in the signal and is typically in the range [m — 1, m + 1] .
  • I is the experimental fluorescence amplitude
  • l is the Poisson parameter (rate)
  • k o is a fitting parameter whose value corresponds to the amplitude associated with a single RBP-bound slncRNA molecule within the burst.
  • the immediate surroundings of each discovered bright spot are recorded as a sub-frame containing the spot at its center, from this sub-frame the mean spot intensity and mean background intensity are calculated.
  • the selection of the sub-frame length used to calculate the background intensity is an important parameter in the analysis process that might bring about unwanted noise into the resulting statistics when analyzing in vivo images.
  • a large sub-frame might include other cells, with possibly different bright spots of themselves, inserting a bias into both the cell background intensity, and spot intensity signals.
  • a small sub-frame might not have a sufficient spot-to-background area ratio, resulting in an underestimated cell background signal.
  • Fig. 17A shows an example of this where the squares correspond to sub-frames of 10,14 and 20 pixels in length, and the panel itself constitutes a 30-pixel wide sub-frame.
  • the criteria for this selection process are the mean ratio between cell area to spot area; percentage of frames where this ratio is less than one; and the ratio between the spot mean intensity to the cell mean intensity without any filtering or fitting. These criteria are designed to find the length that does not cause an overestimation of cell background against spot or vice versa (as could be the case where more than one bright spot fall inside the sub-frame).
  • the moving average window span is a critical component in the signal analysis process. It is used both as a noise reduction filter, and as a means to bias sharp signal jumps.
  • the filter span plays another significant role, as it is the minimal allowed length for a burst duration. Choosing a small value might introduce false positives into the statistics, while a large value would cause many actual burst events to be discarded.
  • To find the optimal span length we compare the number of events found in a simulated flat signal, such a signal should not produce any bursts under noise-less conditions. For this we simulated 1000 constant signals, 360 time points each, with an added white Gaussian noise and an exponential component and applied our data analysis procedure. (Fig. 18A). An ideal result for this test would be less than one event of each type, i.e., positive, and negative bursts, per signal (Fig. 18B).
  • This protocol was designed to have the test articles (slncRNA molecules, ACE2F proteins, and antiviral SRNP granule solutions) inoculated with two different betacorona viruses: delta and omicron variants of SARS-CoV-2. The experiment was run with the Delta variant, followed by the Omicron variant.
  • the infection media was prepared as follows for each virus. 52.5 m ⁇ of test article 1 was added in triplicate to row A (col 1-3), 52.5 m ⁇ of test article 2 was added in triplicate to row A (col 4-6); and 52.5 m ⁇ of test article 3 was added in triplicate to row A (col 7-9). 52.5 m ⁇ infection media (M199 (Gibco, 41150087) + 0.3% BSA) was added to untreated infected, untreated uninfected, and media controls (col 10, 11, and 12 respectively). Using a multichannel pipette, 35m1 of infection media was added to all wells of the plates except row A. 17.5 m ⁇ was transferred from row A to row B ensuring no contamination across columns. This was repeated until row H.
  • Virus-test-article solution was incubated for 1 hr in a humidified incubator.
  • slncRNA elicits no substantial antiviral response at low concentrations for both variants, and potentially a non-specific effect at higher concentrations (Figs. 25D and 25E).
  • the enhancement suggests that the infection process is "primed". "Primed” means that prior to virus activation, one or more ACE2-spike binding events must occur.
  • the results (Fig. 25C) show that at two priming steps and above enhancement of infection occurs in a fashion that is similar to that observed in the experiments for delta. This is consistent with the spike protein being a trimer suggesting that three ACE2 binding events must occur before the virus becomes activated.
  • our anticorona granules constitute a potential therapeutic that can prevent infection and/or severe illness in any SARS2 variant or other betacorona virus disease (e.g. SARS).
  • V°, V i and V n correspond to the unprimed, i th -stcp, and n th -step primed virus concentration respectively.
  • T and C correspond to the therapeutic and uninfected cell concentrations respectively.
  • C * corresponds to infected cell concentration which can create new unprimed virus particles at a rate a.
  • K v is the virus binding affinity to ACE2 (either as a therapeutic or on the cell)
  • k is the rate at which the virus binds ACE2
  • g corresponds to a spontaneous reversion to a previous primed state.
  • the priming equations are then complemented by the following activation equations:
  • V d corresponds to the concentration of deactivated virus particles as a result of the decoy therapeutic
  • C T is a constant corresponding to the total cell concentration in the experiment.
  • RNAse-free water ACE2F-granule low 100ul RNAse-free water ACE2F-granule low:
  • RNAse-free water 220m1 lOO ⁇ g/mI RNA stock of 1:1 (200 ⁇ g/ ⁇ l RNA stock in RNAse-free water):(RNAse-free water).
  • slncRNA for all samples could be detected on Day 1 and Day 3 after injection, and in particular, the higher and lower initial concentration for both ACE2F- granules and tdPP7-granules could be differentiated.
  • the samples rapidly degraded only after Day 3.
  • the higher concentration of tdPP7-granules appeared to be detectible on Day 7 and Day 10.
  • one sample was detected beyond day 3 (day 7). It should be noted that none of those samples were detected in the other replicates after day 3 thus indicating that only a trace amount (akin to a digital PCR) was detected.
  • Example 7 Microneedle delivery of anti-SARS-CoV-2 SRNP granules.
  • microneedle formulations were developed for the purpose of protein and RNA drug delivery.
  • the research formulation composition developed protects the anticorona SRNP granules and mimics several dissolution profiles of drug delivery into the blood stream. Profiles of different formulations (suitable for administration) are provided in Fig. 27.
  • Fig. 27 provides a dissolution profile for the synthetic RNA-protein granules.
  • the microneedles have been made for laboratory purposes out of polydimethylsiloxane to make a master structure that will be the basis of the formed transdermal patch and microneedles. The mold was then filled with two different formulations. One formulation was created using a sustained release with PEG, while the other leveraged PLGA.
  • Profile two is similar to the dosing profile generated by the protocol used for the two-dose COVID-19 vaccines (i.e. Pfizer, Modema, and Astra-Zenica).
  • Profile three top-right, Fig. 27
  • profile four bottom-right
  • profile four is a gradual dose of drug from initial administration until depletion. It is important to note that the best delivery profile for the antriviral SRNP granules may be different than what is used for the two-dose vaccines that have already been approved.
  • the drug delivery would be dissolved within the blood stream and eliminated from the body upon depletion of the drug within the delivery vehicle.

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Abstract

L'Invention concerne des granules d'ARN-protéine comprenant des protéines de fusion et de l'ARN, ainsi que leurs utilisations pour le traitement ou la prévention d'une infection virale. L'invention concerne des protéines de fusion solubles comprenant un domaine extracellulaire d'un récepteur humain ou d'un fragment de celui-ci et une protéine de revêtement bactériophage, ainsi que des microsupports synthétiques comprenant un support solide conjugué à une pluralité de protéines virales ou de fragments de celles-ci. L'invention concerne également des molécules d'acide nucléique et des vecteurs codant pour la protéine de fusion soluble, des granules synthétiques d'ARN-protéine comprenant une protéine de fusion, ainsi qu'un procédé utilisant la protéine de fusion soluble.
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